Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

Defect-Facilitated Buckling in Supercoiled Double-Helix DNA

We present a statistical-mechanical model for stretched twisted double-helix DNA, where thermal fluctuations are treated explicitly from a Hamiltonian without using any scaling hypotheses. Our model applied to defect-free supercoiled DNA describes coexistence of multiple plectoneme domains in long DNA molecules at physiological salt concentrations (≈ 0.1 M Na+) and stretching forces (≈ 1 pN). We find higher (lower) number of domains at lower (higher) ionic strengths and stretching forces, in accord with experimental observations. We use our model to study the effect of an immobile point defect on the DNA contour that allows a localized kink. The degree of the kink is controlled by the defect size, such that a larger defect further reduces the bending energy of the defect-facilitated kinked end loop. We find that a defect can spatially pin a plectoneme domain via nucleation of a kinked end loop, in accord with experiments and simulations. Our model explains previously-reported magnetic tweezer experiments [1] showing two buckling signatures: buckling and ‘rebuckling’ in supercoiled DNA with a base-unpaired region. Comparing with experiments, we find that under 1 pN force, a kinked end loop nucleated at a base-mismatched site reduces the bending energy by ≈ 0.7 kBT per unpaired base. Our model predicts coexistence of three states at the buckling and rebuckling transitions that warrants new experiments.

Essential role for polymerase specialization in cellular nonhomologous end joining

Nonhomologous end joining (NHEJ) repairs chromosome breaks and must remain effective in the face of extensive diversity in broken end structures. We show here that this flexibility is often reliant on the ability to direct DNA synthesis across strand breaks, and that polymerase (Pol) μ and Pol λ are the only mammalian DNA polymerases that have this activity. By systematically varying substrate in cells, we show each polymerase is uniquely proficient in different contexts. The templating nucleotide is also selected differently, with Pol μ using the unpaired base adjacent to the downstream 5′ phosphate even when there are available template sites further upstream of this position; this makes Pol μ more flexible but also less accurate than Pol λ. Loss of either polymerase alone consequently has clear and distinguishable effects on the fidelity of repair, but end remodeling by cellular nucleases and the remaining polymerase helps mitigate the effects on overall repair efficiency. Accordingly, when cells are deficient in both polymerases there is synergistic impact on NHEJ efficiency, both in terms of repair of defined substrates and cellular resistance to ionizing radiation. Pol μ and Pol λ thus provide distinct solutions to a problem for DNA synthesis that is unique to this pathway and play a key role in conferring on NHEJ the flexibility required for accurate and efficient repair.