DNA End Resection:Facts and Mechanisms

DNA double-strand breaks（DSBs）,which arise following exposure to a number of endogenous and exogenous agents,can be repaired by either the homologous recombination（HR）or non-homologous end-joining（NHEJ） pathways in eukaryotic cells.A vital step in HR repair is DNA end resection,which generates a long 30single-stranded DNA（ss DNA） tail that can invade the homologous DNA strand.The generation of 30 ss DNA is not only essential for HR repair,but also promotes activation of the ataxia telangiectasia and Rad3-related protein（ATR）.Multiple factors,including the MRN/X complex,C-terminal-binding protein interacting protein（Ct IP）/Sae2,exonuclease 1（EXO1）,Bloom syndrome protein（BLM）/Sgs1,DNA2 nuclease/helicase,and several chromatin remodelers,cooperate to complete the process of end resection.Here we review the basic machinery involved in DNA end resection in eukaryotic cells.

Assembly of long DNA sequences using a new synthetic Escherichia coli-yeast shuttle vector

Synthetic biology is a newly developed field of research focused on designing and rebuilding novel biomolecular components, circuits, and networks. Synthetic biology can also help understand biological principles and engineer complex artificial metabolic systems. DNA manipulation on a large genome-wide scale is an inevitable challenge, but a necessary tool for synthetic biology. To improve the methods used for the synthesis of long DNA fragments, here we constructed a novel shuttle vector named p GF(plasmid Genome Fast) for DNA assembly in vivo. The BAC plasmid p CC1 BAC, which can accommodate large DNA molecules, was chosen as the backbone. The sequence of the yeast artificial chromosome(YAC) regulatory element CEN6-ARS4 was synthesized and inserted into the plasmid to enable it to replicate in yeast. The selection sequence HIS3, obtained by polymerase chain reaction(PCR) from the plasmid p BS313, was inserted for screening. This new synthetic shuttle vector can mediate the transformation-associated recombination(TAR) assembly of large DNA fragments in yeast, and the assembled products can be transformed into Escherichia coli for further amplification. We also conducted in vivo DNA assembly using p GF and yeast homologous recombination and constructed a 31-kb long DNA sequence from the cyanophage PP genome. Our findings show that this novel shuttle vector would be a useful tool for efficient genome-scale DNA reconstruction.

The archaeal KEOPS complex possesses a functional Gon7 homolog and has an essential function independent of the cellular t^(6)A modification level

Kinase,putative Endopeptidase,and Other Proteins of Small size(KEOPS)is a multisubunit protein complex conserved in eukaryotes and archaea.It is composed of Pcc1,Kae1,Bud32,Cgi121,and Gon7 in eukaryotes and is primarily involved in N^(6)-threonylcarbamoyl adenosine(t^(6)A)modification of transfer RNAs(tRNAs).Recently,it was reported that KEOPS participates in homologous recombination(HR)repair in yeast.To characterize the KEOPS in archaea(aKEOPS),we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus.We show that aKEOPS also possesses five subunits,Pcc1,Kae1,Bud32,Cgi121,and Pcc1-like(or Gon7-like),just like eukaryotic KEOPS.Pcc1-like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric subcomplex(Kae1-Pcc1-Pcc1-Kae1),suggesting that Pcc1-like is a functional homolog of the eukaryotic Gon7 subunit.Strikingly,none of the genes encoding aKEOPS subunits,including Pcc1 and Pcc1-like,can be deleted in the wild type and in a t^(6)A modification complementary strain named TsaKI,implying that the aKEOPS complex is essential for an additional cellular process in this archaeon.Knock-down of the Cgi121 subunit leads to severe growth retardance in the wild type that is partially rescued in TsaKI.These results suggest that aKEOPS plays an essential role independent of the cellular t^(6)A modification level.In addition,archaeal Cgi121 possesses dsDNA-binding activity that relies on its tRNA 3ʹCCA tail binding module.Our study clarifies the subunit organization of archaeal KEOPS and suggests an origin of eukaryotic Gon7.The study also reveals a possible link between the function in t^(6)A modification and the additional function,presumably HR.