The replication fork's five degrees of freedom, their failure and genome rearrangements.

Genome rearrangements are important in pathology and evolution. The thesis of this review is that the genome is in peril when replication forks stall, and stalled forks are normally rescued by error-free mechanisms. Failure of error-free mechanisms results in large-scale chromosome changes called gross chromosomal rearrangements, GCRs, by the aficionados. In this review we discuss five error-free mechanisms a replication fork may use to overcome blockage, mechanisms that are still poorly understood. We then speculate on how genome rearrangements may occur when such mechanisms fail. Replication fork recovery failure may be an important feature of the oncogenic process. (Feedback to the authors on topics discussed herein is welcome.).

Closing the gaps among a web of DNA repair disorders.

As recently as six years ago, three human diseases with similar phenotypes were mistakenly believed to be caused by a single genetic defect. The three diseases, Ataxia-telangiectasia, Nijmegen breakage syndrome, and an AT-like disorder are now known, however, to have defects in three separate genes: ATM, NBS1, and MRE11. Furthermore, new recent studies have shown now that all three gene products interact; the ATM kinase phosphorylates NBS1, which, in turn, associates with MRE11 to regulate DNA repair. Remarkably or expectedly, depending on one's point of view, the similarity in disease phenotypes is evidently due to defects in a common DNA repair pathway.

RAD53, DUN1 and PDS1 define two parallel G2/M checkpoint pathways in budding yeast.

Eukaryotic checkpoint genes regulate multiple cellular responses to DNA damage. In this report, we examine the roles of budding yeast genes involved in G2/M arrest and tolerance to UV exposure. A current model posits three gene classes: those encoding proteins acting on damaged DNA (e.g. RAD9 and RAD24), those transducing a signal (MEC1, RAD53 and DUN1) or those participating more directly in arrest (PDS1). Here, we define important features of the pathways subserved by those genes. MEC1, which we find is required for both establishment and maintenance of G2/M arrest, mediates this arrest through two parallel pathways. One pathway requires RAD53 and DUN1 (the 'RAD53 pathway'); the other pathway requires PDS1. Each pathway independently contributes approximately 50% to G2/M arrest, effects demonstrable after cdc13-induced damage or a double-stranded break inflicted by the HO endonuclease. Similarly, both pathways contribute independently to tolerance of UV irradiation. How the parallel pathways might interact ultimately to achieve arrest is not yet understood, but we do provide evidence that neither the RAD53 nor the PDS1 pathway appears to maintain arrest by inhibiting adaptation. Instead, we think it likely that both pathways contribute to establishing and maintaining arrest.

Yeast checkpoint controls and relevance to cancer.

Checkpoint controls arrest cells with defects in DNA replication or DNA damage. For several reasons, checkpoint controls may be relevant to ontogeny and treatment of cancer. Firstly, mutations in two human genes, TP53 and ATM, give rise to cellular defects in cell cycle checkpoints and are associated with cancer. Secondly, although checkpoint defects potentially render the cell damage sensitive, they may do so only in combination with other defects in the cell's response to damage. Therefore, manipulation of checkpoint defects, requiring a description of normal and mutant pathways, will be required for this type of therapeutic approach. Those pathways are being described in yeast cells. In budding yeast, the study of checkpoint genes has led to the view that these genes have many roles in the cellular responses to DNA damage, including roles in arrest in multiple stages of cell cycle, in transcriptional induction of repair genes, in DNA repair itself and additionally some undefined role in DNA replication. The checkpoint pathways and proteins that carry out these responses may consist of sensor proteins that detect damage, signaller proteins that transduce an inhibitory signal and target proteins that are altered to arrest cell division (or cause other changes in cell behaviour). Yeast genes that may act at each step have been identified, leading to a working model of checkpoint pathways. An initial step in the pathway may involve the processing of damage to an intermediate that signals arrest and acts in DNA repair. Human checkpoint pathways may have defects in processing damage as well.

Cell cycle checkpoints, genetic instability and cancer.

During the cell cycle, the order of events is maintained by controls termed checkpoints. Two checkpoints are sensitive to DNA damage, one that acts before mitosis and a second that acts before DNA replication. This is relevant to cancer because checkpoint mutants show genetic instability, and such instability is characteristic of many cancers. Studies of checkpoints in normal and cancer cells suggest a mechanistic relationship to the central cell cycle control p34CDC2 and its regulators. We suggest how mutations in these genes and those with a role in DNA metabolism may affect the function of checkpoints. A further link between checkpoints and cancer may be the p53 protein, which appears to function at the G1-S checkpoint. Consideration of checkpoints may provide more effective means for cancer treatment.