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1. Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria

   https://doi.org/10.1073/pnas.2002933117  

   Wu, Xiaolin; Cao, Bo; Aquino, Patricia; Chiu, Tsu-Pei; Chen, Chao; Jiang, Susu; Deng, Zixin; Chen, Shi; Rohs, Remo; Wang, Lianrong; et al (June 2020, Proceedings of the National Academy of Sciences)

   Phosphorothioate (PT) DNA modifications—in which a nonbonding phosphate oxygen is replaced with sulfur—represent a widespread, horizontally transferred epigenetic system in prokaryotes and have a highly unusual property of occupying only a small fraction of available consensus sequences in a genome. UsingSalmonella entericaas a model, we asked a question of fundamental importance: How do the PT-modifying DndA-E proteins select their G_PSAAC/G_PSTTC targets? Here, we applied innovative analytical, sequencing, and computational tools to discover a novel behavior for DNA-binding proteins: The Dnd proteins are “parked” at the G^6mATC Dam methyltransferase consensus sequence instead of the expected GAAC/GTTC motif, with removal of the^6mA permitting extensive PT modification of GATC sites. This shift in modification sites further revealed a surprising constancy in the density of PT modifications across the genome. Computational analysis showed that GAAC, GTTC, and GATC share common features of DNA shape, which suggests that PT epigenetics are regulated in a density-dependent manner partly by DNA shape-driven target selection in the genome. 

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2. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps

   https://doi.org/10.1002/ece3.6640  

   Hill, Geoffrey E. (August 2020, Ecology and Evolution)

   Abstract DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination. 

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3. The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity

   https://doi.org/10.3389/fmicb.2021.657356  

   Zatopek, Kelly M.; Burkhart, Brett W.; Morgan, Richard D.; Gehring, Alexandra M.; Scott, Kristin A.; Santangelo, Thomas J.; Gardner, Andrew F. (May 2021, Frontiers in Microbiology)

   Thermococcus kodakarensis ( T. kodakarensis ), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites. In this work, we demonsrate T. kodakarensis strains deleted for either or both R-M enzymes grow more slowly but display significantly increased competency compared to strains with intact R-M systems, suggesting that both TkoI and TkoII assist in maintenance of genomic integrity in vivo and likely protect against viral- or plasmid-based DNA transfers. Pacific Biosciences single molecule real-time (SMRT) sequencing of T. kodakarensis strains containing both, one or neither R-M systems permitted assignment of the recognition sites for TkoI and TkoII and demonstrated that both R-M enzymes are TypeIIL; TkoI and TkoII methylate the N 6 position of adenine on one strand of the recognition sequences GTGA A G and TTCA A G, respectively. Further in vitro biochemical characterization of the REase activities reveal TkoI and TkoII cleave the DNA backbone GTGAAG(N) 20 /(N) 18 and TTCAAG(N) 10 /(N) 8 , respectively, away from the recognition sequences, while in vitro characterization of the MTase activities reveal transfer of tritiated S-adenosyl methionine by TkoI and TkoII to their respective recognition sites. Together these results demonstrate TkoI and TkoII restriction systems are important for protecting T. kodakarensis genome integrity from invading foreign DNA. 

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4. Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

   https://doi.org/10.1093/nar/gkaa206  

   Spealman, Pieter; Burrell, Jaden; Gresham, David (April 2020, Nucleic Acids Research)

   Abstract Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavior characterized by low confidence, incorrect and missed base calls. Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased sampling rates. The coincidence of inverted duplicated DNA sequences with dramatically reduced sequencing accuracy and an increased translocation rate suggests that secondary DNA structures may interfere with the dynamics of transit of the DNA through the nanopore. 

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5. Toward scalable fabrication of electrochemical paper sensor without surface functionalization

   https://doi.org/10.1038/s41528-022-00143-1  

   Wang, Cheng; Wu, Rui; Ling, Hao; Zhao, Zhiling; Han, Wenjia; Shi, Xiaowen; Payne, Gregory F.; Wang, Xiaohui (December 2022, npj Flexible Electronics)

   Abstract Paper-based electrochemical sensors provide the opportunity for low-cost, portable and environmentally friendly single-use chemical analysis and there are various reports of surface-functionalized paper electrodes. Here we report a composite paper electrode that is fabricated through designed papermaking using cellulose, carbon fibers (CF), and graphene oxide (GO). The composite paper has well-controlled structure, stable, and repeatable properties, and offers the electrocatalytic activities for sensitive and selective chemical detection. We demonstrate that this CF/GO/cellulose composite paper can be reduced electrochemically using relatively mild conditions and this GO reduction confers electrocatalytic properties to the composite paper. Finally, we demonstrate that this composite paper offers sensing performance (sensitivity and selectivity) comparable to, or better than, paper-based sensors prepared by small-batch surface-modification (e.g., printing) methods. We envision this coupling of industrialized papermaking technologies with interfacial engineering and electrochemical reduction can provide a platform for single-use and portable chemical detection for a wide range of applications. 

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