Linear Chromosomal DNA Research Articles

The extrachromosomal circular DNA atlas of aged and young mouse brains

Extrachromosomal circular DNA (eccDNA) refers to a distinct class of circular DNA molecules that exist independently from linear chromosomal DNA. Extensive evidence has firmly established the significant involvement of eccDNA in cancer initiation, progression, and evolutionary processes. However, the relationship between eccDNA and brain aging remains elusive. Here, we employed extrachromosomal circular DNA sequencing (Circle-seq) to generate a comprehensive dataset of eccDNA from six brain structures of both young and naturally-aged mice, including the olfactory bulb, medial prefrontal cortex, nucleus accumbens, caudate putamen, hippocampus, and cerebellum. Furthermore, through database annotation, we characterized the properties of mouse brain eccDNA, thereby gaining insights into the potential functions of eccDNA in the mouse brain. In conclusion, our study addresses a previously unexplored area by providing a comprehensive molecular characterization of eccDNA in brain tissues. The data presented in the study can be used as a fundamental resource to associate the molecular phenotypes of eccDNA with brain aging and gain deep insights into the biological role of eccDNA in mammalian brain aging.

Two Sorts of DNA in Eukaryotic Cells: Linear Chromosomal DNA and Circular Extrachromosomal DNA

Two Sorts of DNA in Eukaryotic Cells: Linear Chromosomal DNA and Circular Extrachromosomal DNA

Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA

Extrachromosomal circular DNA (eccDNA) originates from linear chromosomal DNA in various human tissues under physiological and disease conditions. The genomic origins of eccDNA have largely been investigated using invitro-amplified DNA. However, invitro amplification obscures quantitative information by skewing the total population stoichiometry. In addition, the analyses have focused on eccDNA stemming from single-copy genomic regions, leaving eccDNA from multicopy regions unexamined. To address these issues, we isolated eccDNA without invitro amplification (naïve small circular DNA, nscDNA) and assessed the populations quantitatively by integrated genomic, molecular, and cytogenetic approaches. nscDNA of up to tens of kilobases were successfully enriched by our approach and were predominantly derived from multicopy genomic regions including segmental duplications (SDs). SDs, which account for 5% of the human genome and are hotspots for copy number variations, were significantly overrepresented in sperm nscDNA, with three times more sequencing reads derived from SDs than from the entire single-copy regions. SDs were also overrepresented in mouse sperm nscDNA, which we estimated to comprise 0.2% of nuclear DNA. Considering that eccDNA can be integrated into chromosomes, germline-derived nscDNA may be a mediator of genome diversity.

Removal of extracellular free DNA and antibiotic resistance genes from water and wastewater by membranes ranging from microfiltration to reverse osmosis

Free DNA in the effluent from wastewater treatment plants has recently been observed to contain antibiotic resistance genes (ARGs), which may contribute to the spread of antibiotic resistance via horizontal gene transfer in the receiving environment. Technical membrane systems applied in wastewater and drinking water treatment are situated at central nodes between the environmental and human related aspects of the “One Health” approach and are considered as effective barriers for antibiotic resistant bacteria. However, they are not evaluated for their permeability for ARGs encoded in free DNA, which may result, for example, from the release of free DNA after bacterial die-off during particular treatment processes. This study examined the potential and principle mechanisms for the removal of free DNA containing ARGs by technical membrane filtration. Ten different membranes, varied by the charge (neutral and negative) and the molecular weight cut off (in a range from microfiltration to reverse osmosis), were tested for the removal of free DNA (pure supercoiled and linearized plasmids encoding for ARGs and free linear chromosomal DNA with a broader fragment size spectrum) in different water matrices (distilled water and wastewater treatment plant effluent). Our results showed that membranes with a molecular weight cut off smaller than 5000 Da (ultrafiltration, nanofiltration and reverse osmosis) could retain ≥99.80% of free DNA, both pure plasmid and linear fragments of different sizes, whereas microfiltration commonly applied in wastewater treatment showed no retention. Size exclusion was identified as the main retention mechanism. Additionally, surface charging of the membrane and adsorption of free DNA on the membrane surface played a key role in prevention of free DNA permeation. Currently, majority of the applied membranes is negatively charged to prevent adsorption of natural organic matter. In our study, negatively charged membranes showed lower retention of free DNA compared to neutral ones due to repulsion of free DNA molecules, reduced adsorption and decreased blockage of the membrane surface. Therefore, the applied membrane may not be as an effective barrier for ARGs encoded in free DNA, as it would be predicted based only on the molecular weight cut off. Thus, careful considerations of membrane's specifications (molecular weight cut-off and charge) are required during design of a filtration system for retention of free DNA.

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.

Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factorsinduce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatmentwasrequired for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30,HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 1010 cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.

Recognition of Mixed-Sequence DNA Duplexes: Design Guidelines for Invaders Based on 2′-O-(Pyren-1-yl)methyl-RNA Monomers

The development of agents that recognize mixed-sequence double-stranded DNA (dsDNA) is desirable because of their potential as tools for detection, regulation, and modification of genes. Despite progress with triplex-forming oligonucleotides, peptide nucleic acids, polyamides, and other approaches, recognition of mixed-sequence dsDNA targets remains challenging. Our laboratory studies Invaders as an alternative approach toward this end. These double-stranded oligonucleotide probes are activated for recognition of mixed-sequence dsDNA through modification with +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl-RNA monomers and have recently been shown to recognize linear dsDNA, DNA hairpins, and chromosomal DNA. In the present work, we systematically studied the influence that the nucleobase moieties of the 2'-O-(pyren-1-yl)methyl-RNA monomers have on the recognition efficiency of Invader duplexes. Results from thermal denaturation, binding energy, and recognition experiments using Invader duplexes with different +1 interstrand zippers of the four canonical 2'-O-(pyren-1-yl)methyl-RNA A/C/G/U monomers show that incorporation of these motifs is a general strategy for activation of probes for recognition of dsDNA. Probe duplexes with interstrand zippers comprising C and/or U monomers result in the most efficient recognition of dsDNA. The insight gained from this study will drive the design of efficient Invaders for applications in molecular biology, nucleic acid diagnostics, and biotechnology.

Replication arrest is a major threat to growth at low temperature in Antarctic Pseudomonas syringae Lz4W

Chromosomal damage was detected previously in the recBCD mutants of the Antarctic bacterium Pseudomonas syringae Lz4W, which accumulated linear chromosomal DNA leading to cell death and growth inhibition at 4°C. RecBCD protein generally repairs DNA double-strand breaks by RecA-dependent homologous recombination pathway. Here we show that ΔrecA mutant of P. syringae is not cold-sensitive. Significantly, inactivation of additional DNA repair genes ruvAB rescued the cold-sensitive phenotype of ΔrecBCD mutant. The ΔrecA and ΔruvAB mutants were UV-sensitive as expected. We propose that, at low temperature DNA replication encounters barriers leading to frequent replication fork (RF) arrest and fork reversal. RuvAB binds to the reversed RFs (RRFs) having Holliday junction-like structures and resolves them upon association with RuvC nuclease to cause linearization of the chromosome, a threat to cell survival. RecBCD prevents this by degrading the RRFs, and facilitates replication re-initiation. This model is consistent with our observation that low temperature-induced DNA lesions do not evoke SOS response in P. syringae. Additional studies show that two other repair genes, radA (encoding a RecA paralogue) and recF are not involved in providing cold resistance to the Antarctic bacterium.

Transduction of hTR into Hematopoietic Stem Cells Increases Telomerase Activity

Background: Telomerase, an enzyme complex that adds telomere repeats to the ends of linear chromosomal DNA, is an important regulator of cellular senescence and replication. The human telomerase complex is composed of several factors including an RNA component (hTR) that acts as a template, a reverse transcriptase (hTERT), and dyskerin, a stabilizing nuclear protein. Telomerase activity is tightly regulated by hTERT and hTR levels. Several reports have shown that overexpression of hTERT by gene transfer can upregulate telomerase activity in somatic cells, though the effects of hTR gene transfer on telomerase activity in primary cells are unclear. Importantly, mutations in the major components of the telomerase complex cause dyskeratosis congenita (DC), a premature aging syndrome associated with defective hematopoiesis. Of note, our group has recently demonstrated correction of an abnormal phenotype in autosomal dominant (AD) DC fibroblasts by gene transfer of hTR. Additionally, hematopoietic stem cells (HSC) from several AD DC subjects were collected which could be used for future gene therapy studies. In anticipation of these studies, we hypothesized that a lentiviral vector-based gene transfer of hTR into normal hematopoietic stem cells (HSCs) might result in an upregulation of telomerase activity and a corresponding increase in replicative capacity.Methods: CD34 positively selected HSCs isolated from umbilical cord blood were expanded in cytokinesupplemented Stem Span media and counted periodically over a 14-day time course to determine proliferative capacity. Over this time course, cells were assessed for telomerase activity using the TRAP (telomeric repeat amplification protocol) assay. Additionally, cells were plated in a methylcellulose-based media in order to assess colony forming unit (CFU) formation. Transduction of HSCs was accomplished by infecting with a lentiviral (HIV) vector expressing GFP alone or GFP and hTR together. Transduced cells were assessed for GFP expression and then subjected to the same assessments as described above and comparisons were made to non-transduced cells.Results: HSCs cultured in Stem Span showed a 100 fold expansion of total nucleated cells over a 14-day time course. Two days post infection, transduction efficiency of 60% was achieved for CD34+ HSCs transduced with GFP alone, and 10% for hTR/GFP. At nine days post infection there was a similar percentage of GFP-expressing cells, suggesting retention of the construct in differentiated cells. Comparing transduced and non-transduced cells, minimal differences were observed in cell proliferation and colony formation, indicating that conditions used for viral gene transfer did not have a deleterious effect on HSCs. Telomerase activity was markedly increased in hTR-transduced cells at day 2 and 4 post-infection, compared to non-transduced and GFP-transduced cells (18 to 33 fold estimated increase). At later time points post-infection (6 to 10 days), telomerase activity in hTR-transduced cells decreased to levels similar to those of non-transduced cells. Additionally, an accelerated loss of CD34 expression was noted in hTR transduced cells.Conclusions: Lentiviral gene transfer of the hTR component of telomerase into normal HSCs results in an upregulation of telomerase activity without having any noticeable effect on cell proliferation or CFU formation but a possible alteration in differentiation. These studies indicate that transduction of hTR into HSCs may provide a means to upregulate telomerase and potentially correct the proliferative defects observed in bone marrow failure syndromes such as AD DC that are caused by prematurely shortened telomeres.

3'-Azido-2',3'-dideoxynucleoside 5'-triphosphates inhibit telomerase activity in vitro, and the corresponding nucleosides cause telomere shortening in human HL60 cells

Telomerase adds telomeric DNA repeats to the ends of linear chromosomal DNA. 3′-Azido-3′-deoxythymidine 5′-triphosphate (AZTTP) is a known telomerase inhibitor. To obtain more selective and potent inhibitors that can be employed as tools for studying telomerase, we investigated the telomerase-inhibitory effects of purine nucleosides bearing a 3′-down azido group: 3′-azido-2′,3′-dideoxyguanosine (AZddG) 5′-triphosphate (AZddGTP), 3′-azido-2′,3′-dideoxy-6-thioguanosine (AZddSG) 5′-triphosphate (AZddSGTP), 3′-azido-2′,3′-dideoxyadenosine (AZddA) 5′-triphosphate (AZddATP) and 3′-azido-2′,3′-dideoxy-2-aminoadenosine (AZddAA) 5′-triphosphate (AZddAATP). Of these, AZddGTP showed the most potent inhibitory activity against HeLa cell telomerase. AZddGTP was significantly incorporated into the 3′-terminus of DNA by partially purified telomerase. However, AZddGTP did not exhibit significant inhibitory activity against DNA polymerases α and δ, suggesting that AZddGTP is a selective inhibitor of telomerase.We also investigated whether long-term treatment with these nucleosides could alter telomere length and growth rates of human HL60 cells in culture. Southern hybridization analysis of genomic DNA prepared from cells cultured in the presence of AZddG and AZddAA revealed reproducible telomere shortening.

Intraspecific Variability of the Terminal Inverted Repeats of the Linear Chromosome of Streptomyces ambofaciens

The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.

Spontaneous chromosome circularization and amplification of a new amplifiable unit of DNA belonging to the terminal inverted repeats in Streptomyces ambofaciens ATCC 23877.

In Streptomyces, the linear chromosomal DNA is highly unstable and undergoes large rearrangements usually at the extremities. These rearrangements consist of the deletion of several hundred kilobases, often associated with the amplification of an adjacent sequence, AUD ( amplifiable unit of DNA). In Streptomyces ambofaciens, two amplifiable regions (AUD6 and AUD90), located approximately 600 kb and 1,200 kb from the right chromosomal end respectively, have been characterized. Here, the isolation and molecular characterization of a new S. ambofaciens mutant strain exhibiting a green-pigmented phenotype is described; the wild-type produces a gray pigment. In this mutant, both chromosome ends were deleted, which probably led to circularization of the chromosome. These deletions were associated with amplification of a sequence belonging to the chromosomal terminal inverted repeats (TIRs), which might constitute the new fragment generated by the chromosomal circularization.

PCR-based detection of a rare linear DNA in cell culture.

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

Transformation of an oral bacterium via chromosomal integration of free DNA in the presence of human saliva

Transformation of Streptococcus gordonii DL1 by free DNA was studied in human saliva. Competent S. gordonii could be transformed in vitro with plasmid DNA that had been taken into the human mouth. Transformation also occurred with a plasmid that cannot replicate in S. gordonii, but that has a region of chromosomal homology, by integration into the bacterial chromosome, although linearised plasmid DNA gave no transformants. Linear chromosomal DNA fragments did however transform S. gordonii/Tn 916 efficiently in saliva when regions of homology with the recipient chromosome flanked the marker gene. These findings are discussed in relation to the potential for acquisition of DNA sequences, including genetically modified DNA, by gut and oral bacteria.

Transformation of an oral bacterium via chromosomal integration of free DNA in the presence of human saliva.

Transformation of Streptococcus gordonii DL1 by free DNA was studied in human saliva. Competent S. gordonii could be transformed in vitro with plasmid DNA that had been taken into the human mouth. Transformation also occurred with a plasmid that cannot replicate in S. gordonii, but that has a region of chromosomal homology, by integration into the bacterial chromosome, although linearised plasmid DNA gave no transformants. Linear chromosomal DNA fragments did however transform S. gordonii/Tn916 efficiently in saliva when regions of homology with the recipient chromosome flanked the marker gene. These findings are discussed in relation to the potential for acquisition of DNA sequences, including genetically modified DNA, by gut and oral bacteria.

Genome analysis of Agrobacterium tumefaciens: construction of physical maps for linear and circular chromosomal DNAs, determination of copy number ratio and mapping of chromosomal virulence genes.

The phytopathogenic bacterium Agrobacterium tumefaciens is unique in that it possesses both linear and circular DNA chromosomes in addition to a plant-tumor-inducing (Ti) plasmid. We analyzed the two chromosomal DNA molecules in strain MAFF301001, whose Ti plasmid has already been sequenced completely. Physical maps of the chromosomal DNAs were constructed by Southern hybridization experiments using Pme I and Swa I fragments and short fragments bridging the Swa I fragments with special care to avoid any missing fragment. Hybridization with 16S rDNA probe showed one rDNA locus on the linear chromosome and two loci on the circular chromosome. For this bacterium to be pathogenic, not only Ti plasmid but also chromosomal genes are required. The chromosomal virulence (chv) genes (chvA, chvB, chvD, chvE, chvG, chvH, and chvI) and the chromosomal genes affecting the virulence [acvB, pgm(exoC), glgP, miaA, and ros] were successfully mapped onto 5 different regions in the chromosomal physical maps. These chv genes and the chromosomal genes affecting the virulence other than pgm and glgP were found on the circular chromosome, whereas the pgm and glgP genes were located on the linear chromosome. In contrast to the large terminal inverted repeats of Streptomyces linear chromosomal DNA, no hybridization signal was detected between left and right terminal fragments of the linear A. tumefaciens chromosome. Quantitative analysis of DNA fragments indicated that the copy numbers of the two chromosomal DNAs and the Ti plasmid are identical.

Targeting telomeres and telomerase

The ends of eukaryotic chromosomes have unique nucleoprotein structures, termed telomeres, which consist of telomeric DNA and the proteins that bind specifically to these sequences. Telomeric DNA, found in all vertebrates including humans, consists of tandem repeats of the hexanucleotide sequence (TTAGGG) n . The size of telomeric DNA varies among different species, tissues, and cell types, and ranges from a few kilobases (kb) to more than 100 kb. Telomeres are essential for maintaining genomic stability by providing a protective cap for the ends of chromosomes. Other essential function of telomeres in some cells is to prevent the loss of terminal bases at each end of chromosomal DNA following the completion of linear chromosomal DNA replication. It is known that telomerase activity in hematopoietic stem cells in bone marrow is upregulated only when the growth is stimulated by cytokines, whereas resting quiescent cells are essentially telomerase negative. Thus, it was proposed that telomerase-competent stern cells may regulate telomerase activity to maintain levels sufficient to slow but not prevent telomere shortening. The simultaneous downregulation of telomerase and the disruption of telomere maintenance mechanisms by various means might be expected to produce even greater detrimental effects on cancer cell viability.

DNA rearrangements at the extremities of the Streptomyces ambofaciens linear chromosome: Evidence for developmental control

In Streptomyces, a genomic instability results from frequent recombination events which occur at the ends of the linear chromosomal DNA. These events are believed to be responsible for the variability observed in these regions among Streptomyces species and strains. In order to identify functions able to control this type of genome plasticity, mutators as well as mutants produced at different stages of development have been characterized in S. ambofaciens. Their characterization suggests the existence of a relationship between genomic instability and colony development.

Differences between Linear Chromosomal and Supercoiled Plasmid DNA in Their Mechanisms and Extent of Adsorption on Clay Minerals

Plasmid (mainly as the supercoiled form) and linear chromosomal DNA were compared in terms of their mechanisms and degree of adsorption on three clay minerals, kaolinite, montmorillonite, and illite. Based on adsorption isotherms on Ca-clays, adsorption was complete for both plasmid and linear DNA at low concentrations of DNA. Amounts of DNA adsorbed on illite in water were at least 2-fold greater than the amounts adsorbed on kaolinite and montmorillonite, regardless of whether excess divalent Ca (5 mM) was present in the solution. Increasing the concentration of DNA (>25 μg mL-1) increased the adsorption of linear DNA, whereas the adsorption of plasmid DNA molecules decreased, probably as the result of self-aggregation in solution. Titration of acidic groups of DNA showed a narrow range of strong acidity for the plasmid form, whereas the pH of linear chromosomal acidic groups ranged from very low to neutral or slightly alkaline pKa values. The amount of acidic groups per gram of DNA was higher in linear DNA (13.4 cmol g-1) than in supercoiled plasmid DNA (1.8 cmol g-1). Direct observations of plasmid DNA adsorbed on clay minerals by low temperature scanning electron microscopy (LTSEM) indicated that these molecules could act as bridges between clay domains by the ends of the supercoiled molecule. The location and strength of the acidic groups of DNA determine the interaction between clay and DNA. Supercoiled plasmid DNA interacts by a low number of strongly acidic groups, presumably located at the maximum of bending of the double strand where a high charge density exists. Linear chromosomal molecules appear to attach on the clay surface and edges, as demonstrated by previous observations (Paget, E.; et al. FEMS Microbiol Letters 1992, 97, 31), through acidic groups distributed along the DNA molecules. Such differences in interactions between clay and DNA should influence the accessibility to nucleases and persistence of DNA in soil environments.

Chromosome geometry and intraspecific genetic polymorphism in Gram-positive bacteria revealed by pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) proved to be a powerful approach to study bacterial genomics. The genome structure and genetic polymorphism of Gram-positive bacteria from the high G+C (Streptomyces) and low G+C (Streptococcus) groups have been studied. PFGE allowed the estimation of the size of their genome at about 8 Mbp and 1.8 Mbp, respectively, and to get an insight into their chromosome geometry. Thus, physical mapping of the genome of wild-type Streptomyces ambofaciens strains revealed the linearity of the 8 Mbp chromosomal DNA and its typical invertron structure, while the 1.8 Mbp chromosome of Streptococcus thermophilus was shown to be circular. These findings disproved the long-standing idea of universality of bacterial chromosome circularity. In addition, strains belonging to the species S. ambofaciens and S. thermophilus allowed us to characterize the genetic polymorphism at the intraspecific level. Within the S. thermophilus species, comparison of the physical maps showed a relative conservation of gene order as well as restriction sites along the chromosome. In contrast, variable loci were characterized that revealed localized genome rearrangements. The most spectacular of these corresponded to horizontal gene transfer events of sequences. In S. ambofaciens, the physical maps of three isolates pointed to the conservation of the genetic organization. However, a strong polymorphism was observed in the terminal regions of the linear chromosomal DNA. Previous PFGE studies in S. ambofaciens gave proof of a high structural instability of a limited region of the chromosome called unstable region (i.e., DNA rearrangements such as deletions and amplifications). These intraclonal rearrangements create an impressive intraspecific polymorphism of genome size and shape (linear or circular). In both organisms, the DNA rearrangements are restricted to particular regions of the chromosome.