Hairpin structures are the primary amplification products: a novel mechanism for generation of inverted repeats during gene amplification

Short-range inversions: rethinking organelle genome stability: template switching events during DNA replication destabilize organelle genomes

In the organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single-strand-switching or a reciprocal-strand-switching event. Single-strand-switching events lead to intermediates containing Y junctions, whereas reciprocal-strand-switching creates Holliday junctions. Common features in all the described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements.

Palindromes and genomic stress fractures: bracing and repairing the damage

DNA palindromes are a source of instability in eukaryotic genomes but remain under-investigated because they are difficult to study. Nonetheless, progress in the last year or so has begun to form a coherent picture of how DNA palindromes cause damage in eukaryotes and how this damage is opposed by cellular mechanisms. In yeast, the features of double strand DNA interruptions that appear at palindromic sites in vivo suggest that a resolvase-type activity creates the fractures by attacking a palindrome after it extrudes into a cruciform structure. Induction of DNA breaks in this fashion could be deterred through a Center-Break palindrome revision process as investigated in detail in mice. The MRX/MRN likely plays a pivotal role in prevention of palindrome-induced genome damage in eukaryotes.

On the Paucity of Duplicated Genes in Caenorhabditis elegans Operons

Spliced leader trans-splicing is an mRNA maturation process used by a small set of eukaryotes, including the nematode C. elegans, to cap the downstream genes of operons. We analyzed the frequency of duplication of operonic genes in C. elegans and confirmed that they are duplicated less often in the genome than monocistronic genes. Because operons account for about 15% of the genes in C. elegans, this lower duplication frequency might place a large constraint on the plasticity of the genome. Further analyses suggest that this paucity of duplicated genes results from operon organization hindering specific types of gene duplication.

The Structure and Early Evolution of Recently Arisen Gene Duplicates in theCaenorhabditis elegansGenome

The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with ≤10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.

Mechanisms of sod2 gene amplification in Schizosaccharomyces pombe

Gene amplification in eukaryotes plays an important role in drug resistance, tumorigenesis, and evolution. The Schizosaccharomyces pombe sod2 gene provides a useful model system to analyze this process. sod2 is near the telomere of chromosome I and encodes a plasma membrane Na(+)(Li(+))/H(+) antiporter. When sod2 is amplified, S. pombe survives otherwise lethal concentrations of LiCl, and >90% of the amplified sod2 genes are found in 180- and 225-kilobase (kb) linear amplicons. The sequence of the novel joint of the 180-kb amplicon indicates that it is formed by recombination between homologous regions near the telomeres of the long arm of chromosome I and the short arm of chromosome II. The 225-kb amplicon, isolated three times more frequently than the 180-kb amplicon, is a palindrome derived from a region near the telomere of chromosome I. The center of symmetry of this palindrome contains an inverted repeat consisting of two identical 134-base pair sequences separated by a 290-base pair spacer. LiCl-resistant mutants arise 200-600 times more frequently in strains deficient for topoisomerases or DNA ligase activity than in wild-type strains, but the mutant cells contain the same amplicons. These data suggest that amplicon formation may begin with DNA lesions such as breaks. In the case of the 225-kb amplicon, the breaks may lead to a hairpin structure, which is then replicated to form a double-stranded linear amplicon, or to a cruciform structure, which is then resolved to yield the same amplicon.

The papillomavirus E6 proteins

Specific types of human papillomaviruses (HPV) are strongly associated with the development of cervical cancer. The E6 gene from cancer-related HPVs has exhibited functions in tumorigenesis, regulation of transcription, telomerase, and apoptosis. Cancer-related HPVs E6 proteins bind the tumor suppressor p53 and promotes its degradation through an ubiquitin-dependent pathway. Several additional cellular E6-binding proteins have recently been identified and implicated in playing roles in p53-independent functions of E6.

Organization, generation and replication of amphimeric genomes: a review

Genomes comprising a pair of separated inverted repeats and called 'amphimers' are reviewed. Amphimeric genomes are observed in a large variety of different organisms, ranging from archaebacteria to mammals. The widespread existence of amphimeric genomes in nature could be due to their particular dynamic structure. Amphimeric genomes containing long inverted segments may provide the only form in which a duplicated segment is stably retained in genomes. Amphimers are often found in amplified subgenomes, indicating that they could promote a special mechanism of DNA replication and amplification. The possible mechanisms of generation, isomerization and replication/amplification of different types of amphimeric genomes are discussed. The study of amphimeric mitochondrial petite genomes of yeast could be a good model system for the study of the role of inverted repeat sequences in genome dynamics.

A possible role for topoisomerase II in cell death and N-phosphonoacetyl-L-aspartate-resistance frequency and its enhancement by 1-beta-D-arabinofuranosyl cytosine and 5-fluoro-2'-deoxyuridine

Pretreatment of cells with AraC markedly enhances the frequency of resistance to PALA, methotrexate and 5-fluoro-2'-deoxyuridine (FdUrd) (D.V. De Cicco, A.C. Spradling, Localization of a cis-acting element responsible for the developmentally regulated amplification of Drosophila chorion genes. Cell 38 (1984) 45-54). As a part of studies to elucidate the mechanism for this effect of AraC, the SV40 transformed baby hamster kidney cell line SV28 was treated with either AraC, etoposide or etoposide plus verapamil (to avoid selection for P-glycoprotein-mediated resistance) to isolate cells resistant to AraC or etoposide, respectively. The cells isolated for resistance to AraC (500) were cross-resistant to etoposide and the cells isolated for resistance to etoposide (V5ER and 20ER) were cross-resistant to AraC as well as FdUrd (only V5ER were tested). Enhancement of PALA-resistance frequency by pretreatment with various AraC concentrations and exposure times was greatly attenuated in the three resistant cell lines. Pretreatment with FdUrd markedly enhanced PALA-resistance frequency in SV28 cells, but only weakly did so in V5ER cells. All three resistant cell lines had diminished topoisomerase II as measured by immunoblotting and which was reflected in increased LC50s for etoposide. A comparison of either the etoposide LC50 values or the amount of cellular topoisomerase II, as measured by immunoblotting, with the PALA-resistance frequency in the SV28 and resistant cell lines showed a clear correlation. Increased etoposide LC50 or decreased topoisomerase II correlate with increased PALA-resistance frequency. This holds true for cells treated or not pretreated with AraC. Cells with reduced topoisomerase II are more resistant to the lethal actions of not only etoposide, but also AraC and FdUrd, drugs with different primary sites of action. Cells with reduced topoisomerase II have a higher frequency of resistance to PALA by gene amplification and reduced enhancement of gene amplification frequency when treated with AraC or FdUrd. This suggests two different mechanisms responsible for the increased frequency of resistance and the reduced enhancement of resistance frequency, respectively. These data suggest a role for topoisomerase II in cell death and gene amplification. Possible mechanisms are discussed and a scheme is presented.