ABSTRACT
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
Subject(s)
Dictyostelium/genetics , Genome , Genomics , Social Behavior , ATP-Binding Cassette Transporters/genetics , Animals , Base Composition , Cell Adhesion/genetics , Cell Movement/genetics , Centromere/genetics , Conserved Sequence/genetics , DNA Transposable Elements/genetics , DNA, Ribosomal/genetics , Dictyostelium/cytology , Dictyostelium/enzymology , Dictyostelium/metabolism , Eukaryotic Cells/metabolism , Gene Duplication , Gene Transfer, Horizontal/genetics , Humans , Molecular Sequence Data , Phylogeny , Proteome , Protozoan Proteins/chemistry , Protozoan Proteins/genetics , RNA, Transfer/genetics , Repetitive Sequences, Nucleic Acid/genetics , Sequence Analysis, DNA , Signal Transduction/genetics , Telomere/geneticsABSTRACT
RAD53 and MEC1 are essential genes required for the transcriptional and cell cycle responses to DNA damage and DNA replication blocks. We have examined the essential function of these genes and found that their lethality but not their checkpoint defects can be suppressed by increased expression of genes encoding ribonucleotide reductase. Analysis of viable null alleles revealed that Mec1 plays a greater role in response to inhibition of DNA synthesis than Rad53. The loss of survival in mec1 and rad53 null or point mutants in response to transient inhibition of DNA synthesis is not a result of inappropriate anaphase entry but primarily to an inability to complete chromosome replication. We propose that this checkpoint pathway plays an important role in the maintenance of DNA synthetic capabilities when DNA replication is stressed.
Subject(s)
Cell Cycle Proteins , DNA Replication , Protein Serine-Threonine Kinases , S Phase/physiology , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/metabolism , Checkpoint Kinase 2 , DNA Damage , DNA Replication/genetics , DNA, Fungal/biosynthesis , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gene Deletion , Gene Expression , Genes, Fungal , Hydroxyurea/toxicity , Intracellular Signaling Peptides and Proteins , Mitosis/genetics , Mitosis/physiology , Point Mutation , Protein Kinases/genetics , Protein Kinases/metabolism , Ribonucleotide Reductases/genetics , Ribonucleotide Reductases/metabolism , S Phase/genetics , Saccharomyces cerevisiae/genetics , Transcription, GeneticABSTRACT
Mutants of the Saccharomyces cerevisiae ataxia telangiectasia mutated (ATM) homolog MEC1/SAD3/ESR1 were identified that could live only if the RAD53/SAD1 checkpoint kinase was overproduced. MEC1 and a structurally related gene, TEL1, have overlapping functions in response to DNA damage and replication blocks that in mutants can be provided by overproduction of RAD53. Both MEC1 and TEL1 were found to control phosphorylation of Rad53p in response to DNA damage. These results indicate that RAD53 is a signal transducer in the DNA damage and replication checkpoint pathways and functions downstream of two members of the ATM lipid kinase family. Because several members of this pathway are conserved among eukaryotes, it is likely that a RAD53-related kinase will function downstream of the human ATM gene product and play an important role in the mammalian response to DNA damage.
