Article
Biochemistry & Molecular Biology
Joshua A. Sommers, Lorin N. Loftus, Martin P. Jones III, Rebecca A. Lee, Caitlin E. Haren, Adaira J. Dumm, Robert M. Brosh Jr
Summary: This study characterized the catalytic functions and properties of the helicase protein Nsp13 of SARS-CoV-2. It was found that Nsp13 exhibits functional cooperativity and has a preference for single-stranded DNA. The study also revealed the regulatory role of Mg2+ concentration in the catalytic functions of Nsp13.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Anna A. Shiriaeva, Konstantin Kuznedelov, Ivan Fedorov, Olga Musharova, Timofey Khvostikov, Yuliya Tsoy, Elena Kurilovich, Gerald R. Smith, Ekaterina Semenova, Konstantin Severinov
Summary: CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In E. coli, the integration of 33-bp spacers into CRISPR arrays leads to the acquisition of immunity. During the process called primed adaptation, DNA targets complementary to spacers are degraded and serve as a source of new spacers. This study identifies RecJ as the main exonuclease involved in trimming the 5' ends of prespacer precursors, and reveals the functional interactions between genome maintenance proteins and CRISPR interference and adaptation machineries.
Article
Biochemistry & Molecular Biology
Hannah Domgaard, Christian Cahoon, Matthew J. Armbrust, Olivine Redman, Alivia Jolley, Aaron Thomas, Ryan N. Jackson
Summary: CRISPR-associated DinG protein (CasDinG) from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5'-3' DNA translocase that unwinds double-stranded DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a helicase core with three accessory domains. Deletion mutant assays demonstrate that all three domains are essential for type IV-A immunity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jamie Richards, Joel G. Belasco
Summary: In many bacteria, RNase E controls the lifespan of most mRNAs by degrading RNAs with a 5' monophosphate and cleaving them linearly from the 5' terminus. Obstacles encountered along the scanning path of this enzyme, such as bound proteins or ribosomes or base pairing, determine its rate of cleavage at distal sites. We found that the protection provided by these obstacles depends on the size and persistence of the structural discontinuities they create, rather than their molecular composition. Incrementally larger discontinuities have a proportionally greater impact on mRNA stability, suggesting that the effect of obstacles on scanning is not binary.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Yun-Ting Hu, Kai-Xuan Wu, Xiao-Tong Wang, Yuan-Yi Zhao, Xiao-Yong Jiang, Dan Liu, Man-Li Tong, Li-Li Liu
Summary: Tp can invade the central nervous system and evade the immune system, causing neurosyphilis. The study found that Tp can exert toxic effects on microglia by interfering with the autophagosome-lysosome fusion process, leading to the accumulation of autophagosomes and promoting microglial apoptosis. This research provides insights into the immune evasion mechanism of Tp and suggests potential therapeutic strategies for neurosyphilis patients.
Article
Multidisciplinary Sciences
Amitesh Anand, Arjun Patel, Ke Chen, Connor A. Olson, Patrick Phaneuf, Cameron Lamoureux, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. Palsson
Summary: In this study, the authors examined the systems level properties of the aerobic electron transport system using adaptive laboratory evolution and multi-omics analyses.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Vladimir Baytshtok, Xue Fei, Tsai-Ting Shih, Robert A. Grant, Justin C. Santos, Tania A. Baker, Robert T. Sauer
Summary: At low temperatures, protein degradation by the AAA+ HslUV protease is slow due to residues in the intermediate domain of the HslU(6) unfoldase blocking the axial channel, preventing substrate binding and degradation until heat-induced melting of this autoinhibitory plug activates HslUV proteolysis through a model supported by biochemical experiments with wild-type and mutant enzymes.
Article
Biochemistry & Molecular Biology
Justin E. Clarke, Kiran Sabharwal, Louise Kime, Kenneth J. McDowall
Summary: RNase E is an endoribonuclease that plays a crucial role in the maturation of RNA involved in translation and mRNA degradation. It binds to structured RNA elements, activating catalysis and facilitating tRNA processing and potential mRNA degradation. The recognition of structured elements is mediated by a newly discovered groove, essential for E. coli cell viability and distinct from the RNase G family.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Hyejin Oh, Jasung Koo, So Young An, Sung-Hyun Hong, Jeong-Yong Suh, Euiyoung Bae
Summary: The study reveals the molecular mechanism underlying the Gabija anti-phage defense, showing that GajB forms a complex with GajA but does not possess helicase activity on its own.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Kazuki Kato, Sae Okazaki, Cian Schmitt-Ulms, Kaiyi Jiang, Wenyuan Zhou, Junichiro Ishikawa, Yukari Isayama, Shungo Adachi, Tomohiro Nishizawa, Kira S. Makarova, Eugene V. Koonin, Omar O. Abudayyeh, Jonathan S. Gootenberg, Hiroshi Nishimasu
Summary: The type III-E CRISPR-Cas7-11 effector can catalyze crRNA-guided RNA cleavage by binding crRNA and Csx29, and the binding of tgRNA induces conformational changes in Csx29. Csx29 cleaves Csx30 through a tgRNA-dependent pathway, resulting in the generation of toxic protein fragments and growth arrest, which is regulated by Csx31. Csx30 modulates the cellular response to infection by binding Csx31 and the associated sigma factor RpoE. Additionally, the Cas7-11-Csx29-Csx30 system has been engineered for programmable RNA sensing in mammalian cells.
Article
Biochemistry & Molecular Biology
Heidi Zetzsche, Laura Raschke, Boris Fuertig
Summary: In this study, the activation mechanism of RhlB by RNase E was investigated using NMR spectroscopy and an RNA centered approach. The results showed that RNase E binding increases the affinity of RhlB towards certain RNA substrates, leading to increased ATP turnover rates. The study also revealed a unique activation mode of RhlB among DEAD-Box helicases, as it can induce partial duplex opening of RNA even in the absence of ATP.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemical Research Methods
Mikoto Sano, Ryo Tanaka, Kentaro Kamata, Yoko Hirono-Hara, Jun Ishii, Fumio Matsuda, Kiyotaka Y. Hara, Hiroshi Shimizu, Yoshihiro Toya
Summary: This study demonstrated the ATP-consuming conversion of mevalonate to isoprenol using rhodopsin-expressing E. coli cells as a whole-cell catalyst, without energy cosubstrates in the medium. The conversion efficiency was enhanced under light conditions, indicating that ATP regenerated by rhodopsin under light energy can drive the ATP-consuming reactions.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Parinthon Nearmnala, Manutsawee Thanaburakorn, Watanalai Panbangred, Pimchai Chaiyen, Narupat Hongdilokkul
Summary: In this study, a selection system for laboratory evolution of enzymes was engineered by incorporating a translationally suppressing cis repressor and an inducible promoter. Using TEM beta-lactamase as the model enzyme, directed evolution experiments demonstrated a highly active variant with 440-fold improvement in catalytic efficiency. The study also highlighted the importance of the cis repressor in providing sufficient selection pressure for evolving highly efficient enzymes.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Lydia Herzel, Julian A. Stanley, Chun-Chen Yao, Gene-Wei Li
Summary: Bacterial mRNAs have short life cycles with rapid transcription, translation, and degradation processes. The diversity of mRNA molecules at different life-cycle stages impacts their functionality. This study quantitatively maps the 3' status of cellular RNAs in Escherichia coli and reveals that a large fraction of molecules are fragments of full-length mRNAs, with decay intermediates being prevalent. These intermediates are underrepresented in the pool of ribosome-associated transcripts, which may distort analyses of full-length functional mRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jordan Douglas, Remco Bouckaert, Charles W. Carter, Peter R. Wills
Summary: The aminoacyl-tRNA synthetases (AARS) play a crucial role in the evolution of genetic codes by differentiating amino acid side chains and enhancing precision. Simpler catalytic domains are more likely to activate amino acids synthesized at a later stage. The most probable pathway for new amino acids to enter the genetic code is by recruiting low-specificity AARS rather than adapting contemporary ancestors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sk Tofajjen Hossain, Arun Malhotra, Murray P. Deutscher
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Fenghua Yuan, Tanmay Dutta, Ling Wang, Lei Song, Liya Gu, Liangyue Qian, Anaid Benitez, Shunbin Ning, Arun Malhotra, Murray P. Deutscher, Yanbin Zhang
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Sk Tofajjen Hossain, Murray P. Deutscher
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Biochemistry & Molecular Biology
Limin Song, Guangyuan Wang, Arun Malhotra, Murray P. Deutscher, Wenxing Liang
NUCLEIC ACIDS RESEARCH
(2016)
Article
Cell Biology
Douglas R. Boettner, Veronica A. Segarra, Balaji T. Moorthy, Nagore de Leon, John Creagh, John R. Collette, Arun Malhotra, Sandra K. Lemmon
Article
Medicine, Research & Experimental
Lily Liu-Shin, Adam Fung, Arun Malhotra, Gayathri Ratnaswamy
Article
Environmental Sciences
Ivy Mallick, Sk. Tofajjen Hossain, Sangram Sinha, Samir Kumar Mukherjee
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2014)
Article
Biochemistry & Molecular Biology
Tristan Aguero, Zhigang Jin, Dawn Owens, Arun Malhotra, Karen Newman, Jing Yang, Mary Lou King
MOLECULAR REPRODUCTION AND DEVELOPMENT
(2018)
Article
Multidisciplinary Sciences
Brad J. Schmier, Claudiu M. Nelersa, Arun Malhotra
SCIENTIFIC REPORTS
(2017)
Article
Medicine, Research & Experimental
Anja Resemann, Lily Liu-Shin, Guillaume Tremintin, Arun Malhotra, Adam Fung, Fang Wang, Gayathri Ratnaswamy, Detlev Suckau
Article
Medicine, Research & Experimental
Lily Pei-Yao Liu-Shin, Adam Fung, Arun Malhotra, Gayathri Ratnaswamy
Article
Microbiology
Pia Dey, Debaprasad Parai, Malabika Banerjee, Sk Tofajjen Hossain, Samir Kumar Mukherjee
INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY
(2020)