The Effect of Dimethyl Sulfoxide on Supercoiled DNA Relaxation Catalyzed by Type I Topoisomerases

Identification of stimuli that enhance human herpesvirus 6A (HHV-6A) replication and reconstitution

Despite the availability of bacterial artificial chromosome (BAC) systems for human herpesvirus 6A (HHV-6A), reconstitution of infectious viruses is very challenging and time consuming. In this study, we developed approaches to improve the reconstitution process and enhance virus replication to overcome these technical challenges. Using dimethyl sulfoxide and exonuclease V, we significantly increased the efficiency of BAC transfections into JJHan T cells. We tested several stimulation strategies to enhance lytic replication and identified mitogens and glucocorticoids that, in combination, improve virus replication. In addition, we demonstrated that the interferon-mediated response impairs virus reconstitution and that the JAK1/JAK2 inhibitor ruxolitinib resulted in an immense improvement. Furthermore, hypoxia-inducible factor 1 alpha stabilization by IOX2 drastically accelerated virus reconstitution, indicating that the hypoxic response is a crucial regulator of HHV-6A replication. Our study sheds light on strategic approaches that improve replication and reconstitution of this ubiquitous human herpesvirus.

IMPORTANCE

HHV-6A is a betaherpesvirus that infects a wide range of human tissues and establishes lifelong latency in the host. Its reactivation has been implicated in several diseases, including multiple sclerosis, encephalitis, myocarditis, and chronic fatigue syndrome, although its pathogenetic role remains elusive. The efficacy of common antiviral drugs is limited, and no specific drugs target HHV-6A infection. The data of this study shed light on stimuli and potential pathways that influence HHV-6A replication and reconstitution. Our strategies not only simplify virus propagation and reconstitution to study HHV-6A biology but also provide the basis for the development of therapeutic strategies.

Parageobacillus thermoglucosidasius Strain Engineering Using a Theophylline Responsive RiboCas for Controlled Gene Expression

The relentless increase in atmospheric greenhouse gas concentrations as a consequence of the exploitation of fossil resources compels the adoption of sustainable routes to chemical and fuel manufacture based on biological fermentation processes. The use of thermophilic chassis in such processes is an attractive proposition; however, their effective exploitation will require improved genome editing tools. In the case of the industrially relevant chassis Parageobacillus thermoglucosidasius, CRISPR/Cas9-based gene editing has been demonstrated. The constitutive promoter used, however, accentuates the deleterious nature of Cas9, causing decreased transformation and low editing efficiencies, together with an increased likelihood of off-target effects or alternative mutations. Here, we rectify this issue by controlling the expression of Cas9 through the use of a synthetic riboswitch that is dependent on the nonmetabolized, nontoxic, and cheap inducer, theophylline. We demonstrate that the riboswitches are dose-dependent, allowing for controlled expression of the target gene. Through their use, we were then able to address the deleterious nature of Cas9 and produce an inducible system, RiboCas93. The benefits of RiboCas93 were demonstrated by increased transformation efficiency of the editing vectors, improved efficiency in mutant generation (100%), and a reduction of Cas9 toxicity, as indicated by a reduction in the number of single nucleotide polymorphisms (SNPs) observed. This new system provides a quick and efficient way to produce mutants in P. thermoglucosidasius.

Refining our methodologies for assessing quadruplex DNA ligands; selectivity or an illusion of selectivity?

Regulation of transcription and replication by the tetrad patterns of DNA has drawn the attention of many scientists. In this perspective article, we discuss some disparaged parameters in the study of G-quadruplex structures (G4-tetrads). Besides, the implication of "destabilization as a side-effect" by these ligands on quadruplexes is explained. The lack of strict control of in vitro cell-free experiments in terms of ionic concentration, pH, epigenetic modifications, (macro)molecular crowding, and solvent effects is evident in many previous studies. The role of these factors in ligands binding and their possible effects in G-quadruplex structures are also represented.