Error‐free DNA damage tolerance pathway is facilitated by the Irc5 translocase through cohesin

DNA damage tolerance (DDT) mechanisms facilitate replication resumption and completion when DNA replication is blocked by bulky DNA lesions. In budding yeast, template switching (TS) via the Rad18/Rad5 pathway is a favored DDT pathway that involves usage of the sister chromatid as a template to bypass DNA lesions in an error‐free recombination‐like process. Here, we establish that the Snf2 family translocase Irc5 is a novel factor that promotes TS and averts single‐stranded DNA persistence during replication. We demonstrate that, during replication stress, Irc5 enables replication progression by assisting enrichment of cohesin complexes, recruited in an Scc2/Scc4‐dependent fashion, near blocked replication forks. This allows efficient formation of sister chromatid junctions that are crucial for error‐free DNA lesion bypass. Our results support the notion of a key role of cohesin in the completion of DNA synthesis under replication stress and reveal that the Rad18/Rad5‐mediated DDT pathway is linked to cohesin enrichment at sites of perturbed replication via the Snf2 family translocase Irc5.     

Evolution of major metabolic innovations in the Precambrian

A combination of the information on the metabolic capabilities of prokaryotes with a composite phylogenetic tree depicting an overview of prokaryote evolution based on the sequences of bacterial ferredoxin, 2Fe–2S ferredoxin, 5S ribosomal RNA, andc-type cytochromes shows three zones of major metabolic innovation in the Precambrian. The middle of these, which reflects the genesis of oxygenreleasing photosynthesis and aerobic respiration, links metabolic innovations of the anaerobic stem on the one hand and, on the other, proliferation of aerobic bacteria and the symbiotic associations leading to the eukaryotes. We consider especially those pathways where information on the structure of the enzymes is known.Halobacterium andThermoplasma (archaebacteria) do not belong to a totally independent line on the basis of the composite tree but branch from the eukaryote cytoplasmic line.     

Molecular phylogeny of Rodentia in the descent of genusBandicota

The interrelationships of murids and other rodent families as well as the evolutionary descent of multiple β-globins of murines are deduced from parsimony trees of relevant globin sequences. Our results show that Caviidae arises first, followed by Sciuridae which joins Muridae. In the murid line of descent Spalacinae arises first followed by two branches, one representing Cricentinae and Arvicolinae and the other Murinae. Although the rates of evolution of globin genes in the different rodent families are different, the murid branches show more or less a uniform rate of evolution of β globins. We have used this information to show that mouse-rat divergence occurred around 20 million years ago. The evolutionary rationale for the presence and the expression of different β-globin genes in murid populations is also discussed. Based on mitochondrial DNA restriction fragment analysis, the between-species relationships ofRattus rattus rufescens, Bandicota indica andBandicota bengalensis have been assessed and the time of divergence of the two bandicoot rats estimated.     

Spectinomycin resistance mutations in the rrn16 gene are new plastid markers in Medicago sativa

We report here the isolation of spectinomycin-resistant mutants in cultured cells of Medicago sativa line RegenSY-T2. Spectinomycin induces bleaching of cultured alfalfa cells due to inhibition of protein synthesis on the prokaryotic type 70S plastid ribosomes. Spontaneous mutants resistant to spectinomycin bleaching were identified by their ability to form green shoots on plant regeneration medium containing selective spectinomycin concentrations in the range of 25–50?mg/l. Sequencing of the plastid rrn16 gene revealed that spectinomycin resistance is due to mutations in a conserved stem structure of the 16S rRNA. Resistant plants transferred to the greenhouse developed normally and produced spectinomycin-resistant seed progeny. In light of their absence in soybean, a related leguminous plant, the isolation of spectinomycin-resistant mutants in M. sativa was unexpected. The new mutations are useful for the study of plastid inheritance, as demonstrated by detection of predominantly paternal plastid inheritance in the RegenSY-T2?×?Szapko57 cross, and can be used as selective markers in plastid transformation vectors to obtain cisgenic plants.     

The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression

DNA damage must be repaired in an accurate and timely fashion to preserve genome stability. Cellular mechanisms preventing genome instability are crucial to human health because genome instability is considered a hallmark of cancer. Collectively referred to as the DNA damage response, conserved pathways ensure proper DNA damage recognition and repair. The function of numerous DNA damage response components is fine-tuned by posttranslational modifications, including ubiquitination. This not only involves the enzyme cascade responsible for conjugating ubiquitin to substrates but also requires enzymes that mediate directed removal of ubiquitin. Deubiquitinases remove ubiquitin from substrates to prevent degradation or to mediate signaling functions. The Saccharomyces cerevisiae deubiquitinase Ubp7 has been characterized previously as an endocytic factor. However, here we identify Ubp7 as a novel factor affecting S phase progression after hydroxyurea treatment and demonstrate an evolutionary and genetic interaction of Ubp7 with DNA damage repair pathways of homologous recombination and nucleotide excision repair. We find that deletion of UBP7 sensitizes cells to hydroxyurea and cisplatin and demonstrate that factors that stabilize replication forks are critical under these conditions. Furthermore, ubp7Δ cells exhibit an S phase progression defect upon checkpoint activation by hydroxyurea treatment. ubp7Δ mutants are epistatic to factors involved in histone maintenance and modification, and we find that a subset of Ubp7 is chromatin-associated. In summary, our results suggest that Ubp7 contributes to S phase progression by affecting the chromatin state at replication forks, and we propose histone H2B ubiquitination as a potential substrate of Ubp7.