Review
Biochemistry & Molecular Biology
Hao-Hsuan Hsieh, Shu-ou Shan
Summary: The fidelity of protein targeting is crucial for proper organelle functioning. The mechanisms by which cells achieve high accuracy in protein localization are not fully understood. This chapter reviews recent progress in understanding the molecular mechanisms and substrate selection of the SRP pathway in mammals, with a focus on the role of the cotranslational chaperone NAC in protein localization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Donghong Ju, Li Li, Youming Xie
Summary: Ribosomal proteins are regulated by cotranslational protein degradation, which does not require prior ubiquitylation. Cotranslational folding efficiency and expression level are critical factors determining cotranslational protein degradation of ribosomal proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Sung-jun Jung, Ji Eun Hani Kim, Tina Junne, Martin Spiess, Hyun Kim
Summary: This study investigated the targeting and topogenesis of the signal-anchored protein Spc3, finding that it reaches its final topology in two steps: partially dependent on SRP and then mediated by the Sec62/Sec63 complex.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Nanoscience & Nanotechnology
B. S. Joshi, D. Ortiz, I. S. Zuhorn
Summary: Extracellular vesicles (EVs) serve as biological delivery vehicles for therapeutic cargo, with key technologies including loading, surface functionalization, and cargo release methods. Challenges for clinical translation of EV-mediated drug delivery are also discussed.
MATERIALS TODAY NANO
(2021)
Review
Biochemistry & Molecular Biology
Jiri Koubek, Jaro Schmitt, Carla Veronica Galmozzi, Guenter Kramer
Summary: Growing cells dedicate a significant part of their biosynthetic capacity to producing proteins, which must undergo various processes for proper functionality. Integration of translation with protein maturation processes is crucial for efficient and accurate protein synthesis. The interplay of ribosomes, chaperones, and other factors during cotranslational protein maturation guides the sequential events and coupling with protein complex assembly.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Shifeng Wang, Xu Chen, Lauren Crisman, Ximing Dou, Christina S. Winborn, Chun Wan, Harrison Puscher, Qian Yin, Matthew J. Kennedy, Jingshi Shen
Summary: Surface protein levels are regulated by a Reps1-Ralbp1-RalA module in the exocytic pathway. Reps1 and Ralbp1 form a complex that recognizes RalA and promotes exocytosis. Ralbp1 maintains RalA in an active GTP-bound state, stabilizing its GTP state.
Review
Biochemistry & Molecular Biology
Mihaly Badonyi, Joseph A. Marsh
Summary: Recent discoveries have shown that cotranslational assembly is prevalent in proteomes, with various mechanisms enabling the assembly of protein complex subunits on the ribosome. It remains unclear how these complexes have evolved over an extended timescale. This review reflects on historical experiments, breakthroughs in proteome-wide detection of cotranslational assembly, and the remaining technical challenges.
Article
Microbiology
Liuqun Zhao, Yanyan Cui, Gang Fu, Zixiang Xu, Xiaoping Liao, Dawei Zhang
Summary: The signal recognition particle (SRP) is not essential for inner membrane protein (IMP) targeting in E. coli, as suppressor screening identified translation initiation factors that compensate for SRP loss. The time delay in translation initiation plays a critical role in IMP targeting by extending the window for ribosomes to reach the inner membrane.
Review
Biochemistry & Molecular Biology
Hong Wei, Qi Chen, Li Lin, Chunli Sha, Taoqiong Li, Yueqin Liu, Xinming Yin, Yuhao Xu, Lu Chen, Wujiang Gao, Yuefeng Li, Xiaolan Zhu
Summary: Cellular communication through the exchange of biological information, mainly in the form of proteins and RNAs, is mediated by extracellular vesicles like exosomes. Understanding the molecular mechanisms of exosome secretion and cargo sorting is crucial for shedding light on their physiological and pathological functions, as well as for exploring potential therapeutic opportunities in clinical applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Krishnendu Khan, Briana Long, Camelia Baleanu-Gogonea, Valentin Gogonea, Gauravi M. Deshpande, Kommireddy Vasu, Paul L. Fox
Summary: This study reveals that the EBP50-ezrin complex is formed through a cotranslational mechanism, where the C-terminus of mature EBP50 binds to the N-terminal FERM domain of ezrin during mRNA translation. Phosphorylation of EBP50 inhibits this interaction, preventing complex formation. This suggests that eukaryotic mRNA translation plays a role in facilitating complex assembly beyond simply generating linear peptide chains.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Yining Liu, Min Zhao
Summary: This study explores the association between gene dosage effects and gene copy numbers with triple-negative breast cancer using single-cell RNA transcriptome analysis. It reveals that ribosome proteins may play an important role in the stemness and metastatic potential of TNBC.
Article
Cell Biology
Simon Heidegger, Florian Stritzke, Sarah Dahl, Juliane Dassler-Plenker, Laura Joachim, Dominik Buschmann, Kaiji Fan, Carolin M. Sauer, Nils Ludwig, Christof Winter, Stefan Enssle, Suqi Li, Markus Perl, Andre Goergens, Tobias Haas, Erik Thiele Orberg, Sascha Goettert, Catherine Woelfel, Thomas Engleitner, Isidro Cortes-Ciriano, Roland Rad, Wolfgang Herr, Bernd Giebel, Jurgen Ruland, Florian Bassermann, Christoph Coch, Gunther Hartmann, Hendrik Poeck
Summary: Tumor-derived extracellular vesicles (EVs) play a role in immune evasion and tumor progression through the RNA-sensing receptor RIG-I. Activation of RIG-I releases EVs that promote dendritic cell maturation and T cell antitumor immunity, synergizing with immune checkpoint blockade. Intact RIG-I, autocrine interferon signaling, and the GTPase Rab27a are necessary for the generation of immunostimulatory EVs. The composition of the EV RNA cargo, including small non-coding stimulatory RNAs, is regulated by active intrinsic RIG-I signaling. Increased transcriptional activity of EV pathway genes and RIG-I in melanoma samples is associated with prolonged patient survival and positive response to immunotherapy. EVs generated from human melanoma after RIG-I stimulation induce potent antigen-specific T cell responses.
CELL REPORTS MEDICINE
(2023)
Article
Multidisciplinary Sciences
Daphne Mermans, Felix Nicolaus, Klara Fleisch, Gunnar von Heijne
Summary: In recent years, it has been discovered that many cytoplasmic proteins can dimerize while being translated. However, it was unclear whether this phenomenon also applies to integral membrane proteins. This study demonstrates that the inner membrane protein EmrE in Escherichia coli can indeed undergo cotranslational interactions, suggesting that membrane proteins can start to fold and dimerize during the membrane insertion process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Charu Chaudhry
Summary: Proteolysis targeting chimeras (PROTACs) are novel protein degraders that utilize the ubiquitin-proteasome system (UPS) to degrade disease-causing proteins. A mathematical model was developed to study the use of irreversible covalent chemistry in targeted protein degradation (TPD), considering thermodynamic and kinetic factors. The model highlights the advantages of covalency in enhancing ternary complex formation and degradation. Covalent E3 PROTACs show enhanced catalytic efficiency and have the potential to improve the degradation of fast turnover targets.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Cell Biology
Sebastian Eising, Bianca Esch, Mike Waelte, Prado Vargas Duarte, Stefan Walter, Christian Ungermann, Maria Bohnert, Florian Froehlich
Summary: Lysosome is a crucial catabolic organelle in cells, with mutations in lysosomal proteins potentially leading to neurodegeneration, cancer, and age-related diseases. The vacuole serves as a lysosomal analog in Saccharomyces cerevisiae, containing evolutionarily conserved proteins. Proteins can reach vacuoles through different pathways, including the Vps10-dependent endosomal vacuolar protein sorting pathway, the alkaline phosphatase pathway, and the cytosol-to-vacuole transport pathway.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sunil Kumar, Diana E. Schlamadinger, Mark A. Brown, Joanna M. Dunn, Brandon Mercado, James A. Hebda, Ishu Saraogi, Elizabeth Rhoades, Andrew D. Hamilton, Andrew D. Miranker
CHEMISTRY & BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Aileen Ariosa, Jae Ho Lee, Shuai Wang, Ishu Saraogi, Shu-ou Shan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Chemistry, Organic
Oleg V. Kulikov, Sunil Kumar, Mazin Magzoub, Peter C. Knipe, Ishu Saraogi, Sam Thompson, Andrew D. Miranker, Andrew D. Hamilton
TETRAHEDRON LETTERS
(2015)
Article
Chemistry, Multidisciplinary
Oleg V. Kulikov, Yulia V. Sevryugina, Arshad Mehmood, Ishu Saraogi
NEW JOURNAL OF CHEMISTRY
(2017)
Article
Chemistry, Multidisciplinary
Sudipta Ghosh, Snehlata Saini, Ishu Saraogi
CHEMICAL COMMUNICATIONS
(2018)
Review
Biochemistry & Molecular Biology
Ishu Saraogi, Shu-ou Shan
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2014)
Article
Chemistry, Organic
Oleg V. Kulikov, Sam Thompson, Hai Xu, Christopher D. Incarvito, Richard T. W. Scott, Ishu Saraogi, Laura Nevola, Andrew D. Hamilton
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2013)
Article
Chemistry, Multidisciplinary
Ishu Saraogi, Dawei Zhang, Sandhya Chandrasekaran, Shu-ou Shan
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2011)
Review
Biochemistry & Molecular Biology
Ishu Saraogi, David Akopian, Shu-Ou Shan
Article
Medicine, Research & Experimental
Anirban Das, Yogesh M. Gangarde, Viniti Tomar, Omkar Shinde, Tulsi Upadhyay, Sarfaraz Alam, Sudipta Ghosh, Varun Chaudhary, Ishu Saraogi
MOLECULAR PHARMACEUTICS
(2020)
Article
Chemistry, Analytical
Anirban Das, Tanoy Dutta, Laxmikant Gadhe, Apurba Lal Koner, Ishu Saraogi
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Yogesh M. Gangarde, T. K. Sajeev, Nihar R. Panigrahi, Ram K. Mishra, Ishu Saraogi
Article
Chemistry, Multidisciplinary
Bapurao A. Bhoge, Purnima Mala, Jo S. Kurian, Varadharajan Srinivasan, Ishu Saraogi
CHEMICAL COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Vaibhav V. Karekar, Bapurao A. Bhoge, Ishu Saraogi
NEW JOURNAL OF CHEMISTRY
(2019)