In a paper published online in advance in Nucleic Acids Research this week, researchers at Israel's Weizmann Institute of Science and Tel Aviv University show that a "lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism" is a previously unrecognized central barrier to horizontal gene transfer between microbes. In "analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools," the authors write, adding their finding that "similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome."
Researchers at Marshall University in Huntingon, WV, show that "strand bias influences the mechanism of gene editing directed by single-stranded DNA oligonucleotides" in Nucleic Acids Research this week. Using a reductionist approach within a selectable system based on genetic readout in E. coli and plasmids, the team found that "oligonucleotides designed to anneal to the lagging strand generate 100-fold greater 'editing' efficiency than 'those that anneal to' the leading strand."
An international team led by investigators at Harvard Medical School reports basic helix-loop-helix-DNA binding specificity determinants. The team combined its previous array-based C. elegans bHLH-DNA binding specificity data with logics, co-crystal structures, and computational modeling to suggest "which bHLH monomer can interact with which CAN E-box half-site," and to "identify a critical residue in the protein that dictates this specificity." The team suggests that their approach may be a useful took for future "systems-level studies of the DNA binding determinants of other TF families in different model organisms and humans."
CRG Barcelona's Marina Marcet-Houben Toni Gabaldón present TreeKO, "a duplication-aware algorithm for the comparison of phylogenetic trees," in Nucleic Acids Research's online edition. TreeKO "recursively splits gene trees into pruned trees containing only orthologs to subsequently compute a distance based on the combined analyses of all pruned tree comparisons," such that it can compare tree topologies "even in the presence of" gene duplications and losses, Marcet-Houben and Gabaldón write.