Review
Biochemistry & Molecular Biology
Arvind Arul Nambi Rajan, Ben Montpetit
Summary: The DEAD-box protein Dbp5 is a member of the SFII helicase superfamily and plays multiple important roles in gene expression, including regulating mRNA export, non-coding RNA export, translation, transcription, and DNA metabolism. It has the ability to function in different cellular compartments and modulate various stages of RNA lifecycle. Despite over 20 years of research on Dbp5, unanswered questions remain regarding its localization, substrate selection, and mechanistic principles in gene expression.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Shawn Gray, Wenxiang Cao, Ben Montpetit, Enrique M. De La Cruz
Summary: A kinetic and equilibrium analysis of the Gle1-activated Dbp5 ATPase cycle in Saccharomyces cerevisiae reveals that Gle1 activates Dbp5 by modulating ATP binding and P-i release. These findings provide insights into the roles of Gle1 in regulating Dbp5-mediated RNA export and other gene expression functions.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Jiayin Guo, Yaru Zhu, Xiaoya Ma, Guijun Shang, Bo Liu, Ke Zhang
Summary: Gene expression in eukaryotes involves transcription, mRNA synthesis, and mRNA export through the nuclear pore complex (NPC). Viral proteins can interact with host factors involved in mRNA export, leading to inhibition of host gene expression and enhanced viral mRNA export. Understanding these mechanisms can help develop antivirals to inhibit viral mRNA transport and enhance host gene expression, promoting immune responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Cathal S. Ryan, Martina Schroeder
Summary: The human DEAD-box protein DDX3X plays a crucial role in RNA metabolism and has been associated with various diseases, including cancer and neurodevelopmental conditions. It also plays a significant role in viral infections. DDX3X is involved in translation initiation and stress response, and understanding its regulatory mechanisms is important for developing therapeutic strategies.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sarah Venus, Kaba Tandjigora, Eckhard Jankowsky
Summary: The protein K7 from vaccinia virus is shown to inhibit the biochemical activities and cellular functions of DDX3X by binding to its N-terminus, restraining its association with stress granules.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Ravi Shankar Singh, Ananna Bhadra Arna, He Dong, Manisha Yadav, Aanchal Aggarwal, Yuliang Wu
Summary: DDX43, a member of the DEAD-box protein family, exhibits ATP-dependent RNA and DNA helicase activity. Its KH domain selectively binds pyrimidine-rich ssDNA and ssRNA. DDX43 is overexpressed in many tumors and thus holds potential as a target for cancer therapy.
Article
Biochemistry & Molecular Biology
Yeonkyoung Park, Joori Park, Hyun Jung Hwang, Leehyeon Kim, Kwon Jeong, Hyun Kyu Song, Simone C. Rufener, Oliver Muehlemann, Yoon Ki Kim
Summary: It has been demonstrated that CTIF is tethered to the perinuclear region by DDX19B in a translationally incompetent manner, and then handed over to CBP80, which is associated with the 5'-cap of newly exported mRNA, initiating CBC-dependent translation in the perinuclear region. Disrupting the interaction between CTIF and DDX19B leads to uncontrolled translation in the cytosol, ultimately affecting nonsense-mediated mRNA decay. This highlights the importance of tight control of local translation in the perinuclear region.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Pharmacology & Pharmacy
Paul T. Winnard, Farhad Vesuna, Venu Raman
Summary: DDX3X, a multifunctional protein utilized by various viruses, plays a crucial role in viral metabolism. Modulating the functions of DDX3 during viral infections could effectively suppress viral production and have a significant impact on safely and efficiently subduing a broad spectrum of viral infections.
ANTIVIRAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jun-Xiu Wang, En-Bo Ma, Jian-Zhen Zhang, Shu-Ping Xing
Summary: Cellular and molecular mechanisms play a key role in maintaining midgut homeostasis, with LmDDX47 acting as an important regulator by controlling 18S rRNA synthesis and protein modification levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Yaqiong Jin, Jin Shi, Huanmin Wang, Jie Lu, Chenghao Chen, Yongbo Yu, Yaru Wang, Yeran Yang, Dong Ren, Qi Zeng, Xin Ni, Yongli Guo
Summary: The study found that the DDX1 gene polymorphism rs72780850 is associated with an increased risk of NB, especially in aggressive cases. This association may be due to the regulation of DDX1 gene expression affecting tumor risk. Additionally, the molecular mechanism of the rs72780850 polymorphism leading to increased NB risk may be related to the binding affinity of the MAX transcription factor.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Virology
Lisa Wendt, Janine Brandt, Dmitry S. Ushakov, Bianca S. Bodmer, Matthew J. Pickin, Allison Groseth, Thomas Hoenen
Summary: This study reveals the mechanistic details of how Ebola virus (EBOV) and other viruses utilize the nuclear RNA export factor 1 (NXF1) to export viral mRNAs from viral inclusion bodies (IBs). It shows that NXF1 is not only required for the EBOV life cycle but also for other viruses known to replicate in cytoplasmic IBs. These findings suggest NXF1 as a promising target for the development of broadly active antivirals.
JOURNAL OF VIROLOGY
(2022)
Article
Plant Sciences
Chi Xu, Zhanhui Zhang, Juan He, Yongsheng Bai, Jie Cui, Lin Liu, Jihua Tang, Guiliang Tang, Xuemei Chen, Beixin Mo
Summary: RCF1 is shown to play a role in pri-miRNA processing and splicing, as well as pre-mRNA splicing in Arabidopsis thaliana. A mutant with miRNA biogenesis defects was identified, and it was found to be caused by a recessive point mutation in RCF1 (rcf1-4). RCF1 promotes D-body formation and facilitates the interaction between pri-miRNAs and HYL1, and rcf1-4 exhibits a global splicing defect in intron-containing pri-miRNAs and pre-mRNAs. This study uncovers the importance of RCF1 in miRNA biogenesis and RNA splicing in Arabidopsis.
Article
Horticulture
Gangqiang Cao, Huihui Gu, Wenjing Jiang, Zhaoran Tian, Gongyao Shi, Weiwei Chen, Baoming Tian, Xiaochun Wei, Luyue Zhang, Fang Wei, Zhengqing Xie
Summary: This study reveals that the BrDHC1 gene enhances the drought resistance of Brassica rapa, providing new insights and theoretical basis for developing drought-resistant plants.
Article
Multidisciplinary Sciences
Jan Philip Wurm, Katarzyna-Anna Glowacz, Remco Sprangers
Summary: DbpA, an ATP-dependent DEAD-box RNA helicase from Escherichia coli, plays a crucial role in ribosome biogenesis. By binding to hairpin 92 of the 23S rRNA, DbpA's activity is endorsed, indicating its importance in the maturation of ribosomes. The study elucidates how DbpA interacts with maturing ribosomes and the regulatory mechanism that modulates its activity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Lili Zhang, Yanjie Xu, Xuening Liu, Meizhu Qin, Shenglan Li, Tianhua Jiang, Yingjie Yang, Cai-Zhong Jiang, Junping Gao, Bo Hong, Chao Ma
Summary: The chrysanthemum DEAD-box RNA helicase gene CmRH56 plays a role in modulating rhizome outgrowth in response to drought stress by repressing gibberellin biosynthesis.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Bert van Loo, Markus Schober, Eugene Valkov, Magdalena Heberlein, Erich Bornberg-Bauer, Kurt Faber, Marko Hyvoenen, Florian Hollfelder
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Tobias Raisch, Felix Sandmeir, Oliver Weichenrieder, Eugene Valkov, Elisa Izaurralde
JOURNAL OF STRUCTURAL BIOLOGY
(2018)
Article
Chemistry, Multidisciplinary
Bert van Loo, Christopher D. Bayer, Gerhard Fischer, Stefanie Jonas, Eugene Valkov, Mark F. Mohamed, Anastassia Vorobieva, Celine Dutruel, Marko Hyvonen, Florian Hollfelder
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Biochemistry & Molecular Biology
Chung-Te Chang, Sowndarya Muthukumar, Ramona Weber, Yevgen Levdansky, Ying Chen, Dipankar Bhandari, Catia Igreja, Lara Wohlbold, Eugene Valkov, Elisa Izaurralde
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
Tobias Raisch, Chung-Te Chang, Yevgen Levdansky, Sowndarya Muthukumar, Stefan Raunser, Eugene Valkov
NATURE COMMUNICATIONS
(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
Rene M. Arvola, Chung-Te Chang, Joseph P. Buytendorp, Yevgen Levdansky, Eugene Valkov, Peter L. Freddolino, Aaron C. Goldstrohm
NUCLEIC ACIDS RESEARCH
(2020)
Article
Cell Biology
Ramona Weber, Min-Yi Chung, Csilla Keskeny, Ulrike Zinnall, Markus Landthaler, Eugene Valkov, Elisa Izaurralde, Catie Igreja
Article
Biochemistry & Molecular Biology
Isioma I. I. Enwerem, Nathan D. Elrod, Chung-Te Chang, Ai Lin, Ping Ji, Jennifer A. Bohn, Yevgen Levdansky, Eric J. Wagner, Eugene Valkov, Aaron C. Goldstrohm
Summary: PUM1 and PUM2 are sequence-specific RNA-binding proteins essential for vertebrate development and neurological functions. They negatively regulate gene expression by accelerating degradation of specific mRNAs, primarily through direct interaction with the CCR4-NOT complex. These findings reveal a molecular model of repression by PUM1&2 via recruitment of CNOT deadenylation machinery in a decapping-dependent mRNA decay pathway.
Article
Multidisciplinary Sciences
Huaying Zhao, Di Wu, Ai Nguyen, Yan Li, Regina C. Adao, Eugene Valkov, George H. Patterson, Grzegorz Piszczek, Peter Schuck
Summary: The study shows that interactions between the N protein and oligonucleotides lead to the formation of ribonucleoprotein particles. Short oligonucleotide lengths result in compact complexes, while longer lengths promote the formation of higher-order complexes and droplet growth.
Article
Multidisciplinary Sciences
Fabian Poetz, Joshua Corbo, Yevgen Levdansky, Alexander Spiegelhalter, Doris Lindner, Vera Magg, Svetlana Lebedeva, Jorg Schweiggert, Johanna Schott, Eugene Valkov, Georg Stoecklin
Summary: The study identified RNF219 as an acetylation-regulated cofactor of the CCR4-NOT complex, which inhibits mRNA degradation mediated by the complex through interaction with NOT9. RNF219 attenuates global mRNA turnover in cells with a differential requirement of its RING domain.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tobias Raisch, Eugene Valkov
Summary: The conserved CCR4-NOT complex plays a crucial role in initiating mRNA decay by shortening the poly(A) tails. Recent studies have provided insights into its mechanism, including the catalytic and enhancing roles of the enzymatic and non-catalytic subunits, as well as the targeting and control mediated by RNA-binding proteins.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Review
Genetics & Heredity
Shiyang He, Eugene Valkov, Sihem Cheloufi, Jernej Murn
Summary: This review discusses the mechanisms of communication between RBPs and their effectors, and their role in reducing the complexity of RNA networks. The authors highlight the emerging roles of RBP-effector interactions in the control of RNA processing, regulation of biological outcomes, and their contribution to human health and disease.
NATURE REVIEWS GENETICS
(2023)
Article
Multidisciplinary Sciences
Ramona Weber, Leon Kleemann, Insa Hirschberg, Min-Yi Chung, Eugene Valkov, Catia Igreja
Summary: This study reveals the important role of the non-canonical initiation factor DAP5 in selective translation of transcripts, particularly those with long 5' leader sequences and persistent uORF translation. These mRNAs preferentially encode signaling factors, and DAP5 is also involved in translation re-initiation.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Yevgen Levdansky, Tobias Raisch, Justin C. Deme, Filip Pekovic, Hans Elmlund, Susan M. Lea, Eugene Valkov
Summary: This study reveals a conserved module consisting of NOT1, NOT10, and NOT11 in the CCR4-NOT complex, and provides insights into the hierarchical assembly and stabilization of this module. Structural and biochemical characterization of human, chicken, and Drosophila ternary complexes sheds light on its evolutionary conservation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Damien Marchese, Florent Guislain, Tamara Pringels, Laure Bridoux
Summary: Homopolymeric amino acid repeats are common in human proteins, particularly in transcription factors and kinases. This study focuses on homopolymeric histidine repeats (polyH) and their role in regulating embryonic development. Through bioinformatic analysis, the study identifies that polyH-containing proteins interact with cysteine-rich proteins and proteins containing cysteine repeats. The study further investigates the HOXA1 protein, a transcription factor with a long polyH motif, and finds that the polyH motif is necessary for its interaction with cysteine-rich proteins. Additionally, the study discovers that metal ions are required for the HOXA1-MDFI interaction and identifies three polyH interactors that down-regulate the transcriptional activity of HOXA1.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2024)