Because of its stringent sequence specificity, the catalytic domain of the nuclear inclusion protease from tobacco etch virus (TEV) is a useful reagent for cleaving genetically engineered fusion proteins. However, a serious drawback of TEV protease is that it readily cleaves itself at a specific site to generate a truncated enzyme with greatly diminished activity. The rate of autoinactivation is proportional to the concentration of TEV protease, implying a bimolecular reaction mechanism. Yet, a catalytically active protease was unable to convert a catalytically inactive protease into the truncated form. Adding increasing concentrations of the catalytically inactive protease to a fixed amount of the wild-type enzyme accelerated its rate of autoinactivation. Taken together, these results suggest that autoinactivation of TEV protease may be an intramolecular reaction that is facilitated by an allosteric interaction between protease molecules. In an effort to create a more stable protease, we made amino acid substitutions in the P2 and P1' positions of the internal cleavage site and assessed their impact on the enzyme's stability and catalytic activity. One of the P1' mutants, S219V, was not only far more stable than the wild-type protease (approximately 100-fold), but also a more efficient catalyst.

Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency.

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

https://science.sciencemag.org/content/sci/336/6079/341.full.pdf

Synthetic genetic polymers capable of heredity and evolution

Summary: The study of human cytomegalovirus (HCMV) antiviral drug resistance has enhanced knowledge of the virological targets and the mechanisms of antiviral activity. The currently approved drugs, ganciclovir (GCV), foscarnet (FOS), and cidofovir (CDV), target the viral DNA polymerase. GCV anabolism also requires phosphorylation by the virus-encoded UL97 kinase. GCV resistance mutations have been identified in both genes, while FOS and CDV mutations occur only in the DNA polymerase gene. Confirmation of resistance mutations requires phenotypic analysis; however, phenotypic assays are too time-consuming for diagnostic purposes. Genotypic assays based on sequencing provide more rapid results but are dependent on prior validation by phenotypic methods. Reports from many laboratories have produced an evolving list of confirmed resistance mutations, although differences in interpretation have led to some confusion. Recombinant phenotyping methods performed in a few research laboratories have resolved some of the conflicting results. Treatment options for drug-resistant HCMV infections are complex and have not been subjected to controlled clinical trials, although consensus guidelines have been proposed. This review summarizes the virological and clinical data pertaining to HCMV antiviral drug resistance.

Antiviral drug resistance of human cytomegalovirus.

Herpes simplex viruses (HSV) type 1 and type 2 are responsible for recurrent orolabial and genital infections. The standard therapy for the management of HSV infections includes acyclovir (ACV) and penciclovir (PCV) with their respective prodrugs valacyclovir and famciclovir. These compounds are phosphorylated by the viral thymidine kinase (TK) and then by cellular kinases. The triphosphate forms selectively inhibit the viral DNA polymerase (DNA pol) activity. Drug-resistant HSV isolates are frequently recovered from immunocompromised patients but rarely found in immunocompetent subjects. The gold standard phenotypic method for evaluating the susceptibility of HSV isolates to antiviral drugs is the plaque reduction assay. Plaque autoradiography allows the associated phenotype to be distinguished (TK-wild-type, TK-negative, TK-lowproducer, or TK-altered viruses or mixtures of wild-type and mutant viruses). Genotypic characterization of drug-resistant isolates can reveal mutations located in the viral TK and/or in the DNA pol genes. Recombinant HSV mutants can be generated to analyze the contribution of each specific mutation with regard to the drug resistance phenotype. Most ACV-resistant mutants exhibit some reduction in their capacity to establish latency and to reactivate, as well as in their degree of neurovirulence in animal models of HSV infection. For instance, TK-negative HSV mutants establish latency with a lower efficiency than wild-type strains and reactivate poorly. DNA pol HSV mutants exhibit different degrees of attenuation of neurovirulence. The management of ACV- or PCV-resistant HSV infections includes the use of the pyrophosphate analogue foscarnet and the nucleotide analogue cidofovir. There is a need to develop new antiherpetic compounds with different mechanisms of action. Herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) are responsible for recurrent orolabial and genital infections. In the United States, the seroprevalence of HSV-1 and HSV-2 infections has been estimated to be approximately 50% and 20%, respectively (243). Transmission occurs by contact with secretions from an infected person with either overt infection or asymptomatic excretion of virus. After primary infection, HSV establishes long-term latency in the ganglia of sensory nerves, from which it can reactivate episodically. These reactivations may be accompanied by symptoms or may be clinically silent. The most common clinical manifestations of HSV infections are vesicular lesions affecting the mucous membranes principally of the mouth, nose, or eyes for HSV-1 and the anogenital region for HSV-2. However, an increasing proportion of genital infections are caused by HSV-1 (243). The symptoms associated with both viruses are usually self-limiting, and the goals of treatment are to accelerate lesion healing and to prevent transmission in immunocompetent individuals (61). Both HSV-1 and HSV-2 can also cause infrequent but serious diseases, such as encephalitis and disseminated neonatal infections. HSV infections may be severe in immunocompromised patients, particularly those with defects in cell-mediated immunity. In patients with HIV infection and in recipients of solid organ or bone marrow transplants, herpetic lesions can be extensive, tend to persist for longer periods, and have the potential to disseminate. Recurrences tend to be more frequent and may be atypical in appearance (140). In addition to persistent mucocutaneous lesions, HSV can also lead to disseminated visceral infections, such as esophagitis, hepatitis, or pneumonia, as well as meningoencephalitis, in immunocompromised hosts (94, 99, 174).

Resistance of Herpes Simplex Viruses to Nucleoside Analogues: Mechanisms, Prevalence, and Management

DNA polymerase δ (Pol δ) has a crucial role in eukaryotic replication. Now the crystal structure of the yeast DNA Pol δ catalytic subunit in complex with template primer and incoming nucleotide is presented at 2.0-A resolution, providing insight into its high fidelity and a framework to understand the effects of mutations involved in tumorigenesis.

/pdf/structural-basis-of-high-fidelity-dna-synthesis-by-yeast-dna-2rmix3k1uv.pdf

Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta.

Crystal Structure of the Herpes Simplex Virus 1 DNA Polymerase

Recombinant human cytomegalovirus protease with a C-terminal (His)6 extension: purification, autocatalytic release of the mature enzyme, and biochemical characterization.

Eric T. Baldwin

Papers

Crystal Structure of the Herpes Simplex Virus 1 DNA Polymerase

Recombinant human cytomegalovirus protease with a C-terminal (His)6 extension: purification, autocatalytic release of the mature enzyme, and biochemical characterization.

Affinity purification of a chimeric nicotinic acetylcholine receptor in the agonist and antagonist bound states