In a paper published online in advance in Nucleic Acids Research this week, a team led by investigators at Washington University in St. Louis shows that using high-throughput sequencing on transcription factor binding sites recovered via a bacterial one-hybrid — or B1H — system allowed it to generate improved models of binding specificity compared to those it created using "standard methods of sequencing a small subset of the selected clones." In addition, the team reports a new approach to analyze contained variation-B1H data called GRaMS — Growth Rate Modeling of Specificity. "GRaMS analysis is robust to the different experimental parameters whereas other analysis methods give widely varying results depending on the conditions of the experiment," the authors write.
Researchers at the University of Valencia in Spain and the University of Oslo in Norway show that "messenger RNA degradation is initiated at the 5' end and follows sequence- and condition-dependent modes in chloroplasts." More specifically, using reporter gene constructs in the chloroplast of Chlamydomonas reinhardtii, the team found that "the 5′ end of the poly(G) tracts indicating that a 5′→3′ exoribonuclease is involved in the degradation process."
In another Nucleic Acids Research advance online publication, investigators at institutions across Belgium present evidence to suggest that in E. coli, the protein Mrr is involved in a "defense mechanism against the establishment of epigenetic regulation by foreign DNA methyltransferases." Further, the team suggests that evolutionary antagonism exists between Mrr and another endogenous Type III restriction modification system in Salmonella typhimurium LT2.
A team at the St. Louis University School of Medicine reports online in Nucleic Acids Research this week that the recombination mediator protein RecO is recruited to DNA by the single-stranded DNA binding protein SSB. In its comparative analyses, the team found that this mechanism of RecO recruitment varies from organism to organism, such that diverse DNA repair pathways appear to have emerged.