Article
Chemistry, Analytical
Cheng Yang, Yi Yuan, Man Shen, Ke Wang, Hanqing Xu, Yingran Wang, Ming Chen, Jing Bao, Mingxuan Gao
Summary: tRNA-derived small RNA (tsRNA) has been identified as a new biomarker for early diagnosis and prognosis prediction of breast cancer. Researchers have developed a versatile enzymatic reaction called RT-NExT, which can accurately detect the expression levels of tsRNA in a fast and reliable manner.
ANALYTICAL CHEMISTRY
(2022)
Article
Virology
Jerry Joe E. K. Harrison, Steve Tuske, Kalyan Das, Francesc X. Ruiz, Joseph D. Bauman, Paul L. Boyer, Jeffrey J. DeStefano, Stephen H. Hughes, Eddy Arnold
Summary: The crystal structure of mature PR-RT from prototype FV shows that it can carry out protein processing and reverse transcription, but is not competent for enzyme activity. PFV PR-RT is monomeric and shares structural similarities with HIV-1 PR subunits, although it is in a configuration not suitable for enzymatic activity.
Article
Virology
Shogo Nakajima, Koichi Watashi, Takanobu Kato, Masamichi Muramatsu, Takaji Wakita, Noriko Tamura, Shin-ichiro Hattori, Kenji Maeda, Hiroaki Mitsuya, Yoshiaki Yasutake, Tetsuya Toyoda
Summary: By analyzing the resistant mutations in HBV RT, researchers found that ETV-TP may get stuck at M171, leading to the unusual inhibition pattern observed in kinetic analysis. This provides new insights into the mechanism of ETV resistance and suggests potential modifications to enhance the effectiveness of ETV and other nucleos(t)ide analogues as HBV drugs.
JOURNAL OF VIROLOGY
(2021)
Article
Cell Biology
Carl J. Balibar, Daniel J. Klein, Beata Zamlynny, Tracy L. Diamond, Zhiyu Fang, Carol A. Cheney, Jan Kristoff, Meiqing Lu, Marina Bukhtiyarova, Yangsi Ou, Min Xu, Lei Ba, Steven S. Carroll, Abdellatif El Marrouni, John F. Fay, Ashley Forster, Shih Lin Goh, Meigang Gu, Daniel Krosky, Daniel I. S. Rosenbloom, Payal Sheth, Deping Wang, Guoxin Wu, Matthias Zebisch, Tian Zhao, Paul Zuck, Jay Grobler, Daria J. Hazuda, Bonnie J. Howell, Antonella Converso
Summary: Antiretroviral therapy can inhibit HIV-1 replication but cannot cure the infection due to the persistence of a reservoir in the host genome. Reduction of this reservoir is important for HIV-1 cure. Some nonnucleoside reverse transcriptase inhibitors have shown selective cytotoxicity against HIV-1 in vitro, but their concentrations required are much higher than approved dosages. By focusing on this secondary activity, researchers have discovered bifunctional compounds called targeted activators of cell kill (TACK) that can kill HIV-1-infected cells at clinically achievable concentrations. These TACK molecules bind to the reverse transcriptase-p66 domain of monomeric Gag-Pol and act as allosteric modulators, promoting dimerization and premature intracellular viral protease activation, leading to death of HIV-1(+) cells. TACK molecules retain potent antiviral activity and selectively eliminate infected CD4(+) T cells, providing a potential immune-independent clearance strategy.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Anthony J. Rabe, Yow Yong Tan, Ross C. Larue, Kristine E. Yoder
Summary: Different retroviral integrases have varying activity dependent on metal cations, with PFV intasomes uniquely capable of catalysis in calcium and displaying an inverse correlation with manganese concentration. PFV intasomes also show increased activity in the presence of chloride co-ions. This highlights the unique biochemical activities of PFV integrase compared to other retroviral integrases.
Article
Virology
Marzena Nowacka, Elzbieta Nowak, Mariusz Czarnocki-Cieciura, Justyna Jackiewicz, Krzysztof Skowronek, Roman H. Szczepanowski, Birgitta M. Woehrl, Marcin Nowotnya
Summary: Reverse transcriptases are enzymes that play a crucial role in converting single-stranded RNA to double-stranded DNA. Foamy viruses possess a unique reverse transcriptase containing a fusion with a protease domain. This study provides the first structural description of nucleic acid binding by a foamy viral RT, showing its ability to change its oligomeric state depending on the type of bound nucleic acid.
JOURNAL OF VIROLOGY
(2021)
Article
Chemistry, Medicinal
Takumi Yasuno, Tomoyuki Ohe, Hiroki Kataoka, Kosho Hashimoto, Yumiko Ishikawa, Keigo Furukawa, Yasuhiro Tateishi, Toi Kobayashi, Kyoko Takahashi, Shigeo Nakamura, Tadahiko Mashino
Summary: In this study, three novel fullerene derivatives were synthesized, with certain compounds exhibiting inhibitory activity against HIV reverse transcriptase and HIV protease in the low micromolar range. The derivatives with a specific alkyl chain showed more potent inhibition of HIV-PR, suggesting a potential strategy for enhancing HIV-PR inhibitory activity.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Virology
Duygu Tekin, Deniz Gokengin, Huseyin Onay, Selda Erensoy, Ruchan Sertoz
Summary: The study investigated mutations in PR, RT, and IN gene regions of HIV using NGS, and found NGS to be more sensitive and cost-effective compared to SS. Low-frequency resistance mutations were detected in 18.3% of samples, resulting in virological failure in only one patient. The cost of analysis was reduced by sample pooling and multiplex analysis with the MiSeq system.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jirayu Kammarabutr, Panupong Mahalapbutr, Hisashi Okumura, Peter Wolschann, Thanyada Rungrotmongkol
Summary: This study indicates that certain anti-HIV drugs may have higher susceptibility against HBV-RT enzyme, potentially serving as a promising drug option for HBV-infected patients with 3TC resistance.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Diana Angelica Tapia-Sidas, Brenda Yazmin Vargas-Hernandez, Jose Abrahan Ramirez-Pool, Leandro Alberto Nunez-Munoz, Berenice Calderon-Perez, Rogelio Gonzalez-Gonzalez, Luis Gabriel Brieba, Rosalia Lira-Carmona, Eduardo Ferat-Osorio, Constantino Lopez-Macias, Roberto Ruiz-Medrano, Beatriz Xoconostle-Cazares
Summary: The aim of this study was to develop and describe molecular detection systems for SARS-CoV-2 based on RT-LAMP. Recombinant DNA polymerase and reverse transcriptase were purified and used to set up fluorometric real time and colorimetric end-point RT-LAMP assays. The developed RT-LAMP diagnostic tests allowed a sensitive and specific detection of the nucleocapsid gene of SARS-CoV-2.
Article
Plant Sciences
Carlos de Tomas, Carlos M. Vicient
Summary: Endogenous pararetroviruses (EPRVs), derived from DNA viruses of the family Caulimoviridae, are viral sequences integrated into plant genomes. This study analyzed a large number of plant genome sequences and identified 57 clusters and 13 genera of EPRVs, including a newly proposed genus called Wendovirus. There are significant differences in the abundance and distribution of EPRVs between different plant families and genera, with florendoviruses being the most abundant and widespread.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Pharmacology & Pharmacy
Francesc X. Ruiz, Anthony Hoang, Christopher R. Dilmore, Jeffrey J. DeStefano, Eddy Arnold
Summary: Infection with HIV and HBV are major public health problems affecting millions of people globally. The polymerases from both viruses are common drug targets, with drugs like emtricitabine and lamivudine being widely used inhibitors, but details of their binding have remained unknown.
DRUG DISCOVERY TODAY
(2022)
Article
Biochemistry & Molecular Biology
Joshua Yi Yeo, Darius Wen-Shuo Koh, Ping Yap, Ghin-Ray Goh, Samuel Ken-En Gan
Summary: The study found that in an in vitro selection pressure free system, the background mutation rates for Gag, protease, and RT p66 were 4.71 x 10(-5), 6.03 x 10(-5), and 7.09 x 10(-5) mutations/bp, respectively. Gag and p66 genes showed a large number of 'A to G' mutations. Comparison with silently mutated p66 sequences revealed an increase in mutation rates and 'A to G' mutations in regions reminiscent of ADAR neighbor sequence preferences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Ruofan Wang, Ashton T. Belew, Vasudevan Achuthan, Najib El Sayed, Jeffrey J. DeStefano
Summary: Recent analyses have shown that certain subtypes of HIV-1 have higher fidelity in low Mg2+ conditions, while some RTs demonstrate higher fidelity at physiological Mg2+ levels. Sequencing methods have revealed the mutation profiles of HIV-1 RT under different Mg2+ concentrations.
JOURNAL OF GENERAL VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kolin M. Clark, Josh G. Kim, Qiankun Wang, Hongbo Gao, Rachel M. Presti, Liang Shan
Summary: The sensitization of the CARD8 inflammasome to non-nucleoside reverse transcriptase inhibitors (NNRTIs) can be achieved through chemical inhibition of the negative regulator DPP9. The DPP9 inhibitor Val-boroPro (VbP) can kill HIV-1-infected cells without NNRTIs and synergize with NNRTIs to promote clearance of infected cells. This offers a promising strategy for enhancing NNRTI efficacy in eliminating HIV-1 reservoirs.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Cell Biology
Daniel Peter, Ramona Weber, Carolin Koene, Min-Yi Chung, Linda Ebertsch, Vincent Truffault, Oliver Weichenrieder, Catia Igreja, Elisa Izaurralde
GENES & DEVELOPMENT
(2015)
Article
Biochemistry & Molecular Biology
Daniel Peter, Catia Igreja, Ramona Weber, Lara Wohlbold, Catrin Weiler, Linda Ebertsch, Oliver Weichenrieder, Elisa Izaurralde
Article
Biochemistry & Molecular Biology
Stefan Gruener, Daniel Peter, Ramona Weber, Lara Wohlbold, Min-Yi Chung, Oliver Weichenrieder, Eugene Valkov, Catia Igreja, Elisa Izaurralde
Article
Cell Biology
Daniel Peter, Ramona Weber, Felix Sandmeir, Lara Wohlbold, Sigrun Helms, Praveen Bawankar, Eugene Valkov, Catia Igreja, Elisa Izaurralde
GENES & DEVELOPMENT
(2017)
Article
Biochemistry & Molecular Biology
Stefan Gruener, Ramona Weber, Daniel Peter, Min-Yi Chung, Catia Igreja, Eugene Valkov, Elisa Izaurralde
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Christian Seutter von Loetzen, Thomas Hoffmann, Maximilian J. Hartl, Kristian Schweimer, Wilfried Schwab, Paul Roesch, Olivia Hartl-Spiegelhauer
BIOCHEMICAL JOURNAL
(2014)
Article
Biochemistry & Molecular Biology
Philipp R. Weiglmeier, Hanna Berkner, Angela Seebahn, Nico Vogel, Rainer Schreiber, Birgitta M. Woehrl, Stephan Schwarzinger, Paul Roesch
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2014)
Article
Biochemistry & Molecular Biology
Stefanie Jonas, Mary Christie, Daniel Peter, Dipankar Bhandari, Belinda Loh, Eric Huntzinger, Oliver Weichenrieder, Elisa Izaurralde
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2014)
Article
Multidisciplinary Sciences
Catia Igreja, Daniel Peter, Catrin Weiler, Elisa Izaurralde
NATURE COMMUNICATIONS
(2014)
Article
Biochemistry & Molecular Biology
Vincenzo Ruscica, Praveen Bawankar, Daniel Peter, Sigrun Helms, Catia Igreja, Elisa Izaurralde
NUCLEIC ACIDS RESEARCH
(2019)
Article
Cell Biology
Daniel Peter, Vincenzo Ruscica, Praveen Bawankar, Ramona Weber, Sigrun Helms, Eugene Valkov, Catia Igreja, Elisa Izaurralde
GENES & DEVELOPMENT
(2019)
Article
Biochemistry & Molecular Biology
Stavros Beteinakis, Anastasia Papachristodoulou, Peter Kolb, Paul Roesch, Stephan Schwarzinger, Emmanuel Mikros, Maria Halabalaki
Summary: Extra virgin olive oil (EVOO) is highly valued in the food industry and is frequently adulterated. This study used a rapid NMR-based untargeted metabolite profiling method, along with multivariate analysis and statistical total correlation spectroscopy, to determine the origin of EVOO. The results identified chemical classes and biomarkers related to the classification of samples based on their origin.
Article
Biology
Ramona S. Adolph, Eileen Beck, Kristian Schweimer, Andrea Di Fonzo, Michael Weyand, Paul Roesch, Birgitta M. Woehrl, Clemens Steegborn
Summary: Sirtuins are NAD(+)-dependent protein lysine deacylases involved in metabolic regulation and aging-related dysfunctions. Sirt1, a nuclear isoform, deacetylates histones and transcription factors, contributing to brain and immune cell functions. In HIV1 infection, Sirt1 promotes viral genome expression by deacetylating the viral transactivator of transcription (Tat) protein. However, Tat inhibits Sirt1, leading to T cell hyperactivation associated with HIV infection.
