Article
Biology
Mihaly Badonyi, Joseph A. Marsh, Marina Rodnina
Summary: Recent evidence suggests that cotranslational assembly of protein complexes is particularly common between subunits that form large intermolecular interfaces. This study provides further support for this notion and demonstrates that large interfaces have evolved to maximize the chance of successful cotranslational subunit binding.
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
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
Biotechnology & Applied Microbiology
Taolan Zhao, Yan-Ming Chen, Yu Li, Jia Wang, Siyu Chen, Ning Gao, Wenfeng Qian
Summary: The study revealed widespread ribosome collisions in cells, which are associated with slow ribosome release, slow peptide bond formation, and slow leaving of polylysine from the exit tunnel of ribosomes. Collisions occur more frequently in the gap regions between alpha-helices, where translational pauses can prevent interference with protein folding by downstream peptides. Paused or collided ribosomes are associated with specific chaperones, facilitating proper protein folding during translation.
Article
Biochemistry & Molecular Biology
Hena Sandhu, Rickard Hedman, Florian Cymer, Renuka Kudva, Nurzian Ismail, Gunnar von Heijne
Summary: The study reveals that the large periplasmic domain of the E. coli inner membrane protease LepB folds post-translationally in vivo, and demonstrates that Force Profile Analysis (FPA) can be utilized to study both co- and post-translational protein folding in the periplasm.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
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.
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
Ruiyue Tan, Margaret Hoare, Kevin A. Welle, Kyle Swovick, Jennifer R. Hryhorenko, Sina Ghaemmaghami
Summary: The folding of proteins during translation while bound to the ribosome is not well understood. This study developed a method using mass spectrometry to measure the stability of nascent polypeptide chains. The results showed that the ribosome significantly influences the stability of the nascent polypeptides, with variations depending on different folding domains and localized charge distributions within the polypeptides. The study suggests that electrostatic interactions between the ribosome and nascent polypeptides play a role in these stability modulations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Zikun Zhu, Shuai Wang, Shu-ou Shan
Summary: Using ribosome profiling methods, this study elucidates the cotranslational interaction principles of SecA with nascent proteins and reveals a hierarchical organization of protein export pathways in bacteria.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Paul Whitley, Brayan Grau, James C. Gumbart, Luis Martinez-Gil, Ismael Mingarro
Summary: The endoplasmic reticulum (ER) plays a crucial role in eukaryotic cells by facilitating the entry and distribution of newly synthesized proteins. Membrane-integrated amino acids are typically non-polar/hydrophobic and form alpha-helical transmembrane (TM) helices for survival in the ER's non-aqueous environment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Migle Kisonaite, Klemens Wild, Karine Lapouge, Genis Valentin Gese, Nikola Kellner, Ed Hurt, Irmgard Sinning
Summary: The authors used cryo-EM to investigate how the RAC complex, a conserved ribosome-associated chaperone triad, assists in cotranslational protein folding. They determined cryo-EM structures of RAC bound to 80S ribosomes, revealing two distinct conformations and a tight interaction between the RAC components. They also discovered a non-canonical interaction that masks the HPD motif in the J domain protein Zuo1, allowing proper positioning of Ssb for activation. These findings provide insights into the dynamic interaction and protein folding process involving RAC and Ssb.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Evolutionary Biology
Rosa M. Pinto, Albert Bosch
Summary: Codon bias, a common phenomenon in all organisms, is influenced by mutation, drift, and selection. While selection for translation efficiency and accuracy is well recognized, fewer studies have explored the impact of translation rate control on codon usage. Experimental molecular evolution using RNA virus populations is a powerful tool in understanding the mechanisms behind codon bias. Furthermore, experimental studies are encouraged to define the role of selection in codon evolution, as most studies on virus codon usage rely on computational analyses.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Daphne Mermans, Felix Nicolaus, Aysel Baygin, Gunnar von Heijne
Summary: Human growth hormone (hGH) is a protein with four helix bundles and has pharmacological interest. This study investigates the folding of hGH during expression in Escherichia coli, both in vitro translation with or without the chaperone trigger factor (TF) and in E. coli. The findings suggest that hGH begins folding before it is fully released from the ribosome and may interact with TF and other chaperones.
Review
Biochemistry & Molecular Biology
Evan Mercier, Xiaolin Wang, Lena A. K. Boegeholz, Wolfgang Wintermeyer, Marina V. Rodnina
Summary: This review describes recent progress in understanding the processing of nascent peptides and the targeting and orientation of inner-membrane proteins. Biophysical approaches have revealed the dynamics of the translocon and the role of the ribosome in cotranslational targeting and orientation. The review also discusses the auxiliary role of YidC as a chaperone for inner-membrane proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Tatsuya Niwa, Koki Nakazawa, Kensuke Hoshi, Hisashi Tadakuma, Koichi Ito, Hideki Taguchi
Summary: This study investigated the interaction between trigger factor (TF) and nascent polypeptide chains using fluorescence correlation spectroscopy (FCS). The results showed that the interaction between TF and nascent chains depended on the emergence of the nascent chains from the ribosome exit tunnel, and was not inhibited by other chaperones. The translation-dependent interaction between TF and nascent chains was also observed in living cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jiri Koubek, Yet-Ran Chen, Richard Ping Cheng, Joseph Jen-Tse Huang
Article
Chemistry, Multidisciplinary
Charles H. Chen, Ayesha Khan, Joseph Jen-Tse Huang, Martin B. Ulmschneider
CHEMISTRY-A EUROPEAN JOURNAL
(2016)
Article
Multidisciplinary Sciences
Yuan-Peng Du, Hsun-Hui Chang, Sheng-Yu Yang, Shing-Jong Huang, Yu-Ju Tsai, Joseph Jen-Tse Huang, Jerry Chun Chung Chan
SCIENTIFIC REPORTS
(2016)
Article
Biochemistry & Molecular Biology
Jiri Koubek, Yi-Che Chang, Sunny Yao-Chen Yang, Joseph Jen-Tse Huang
JOURNAL OF MOLECULAR BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Devi Wahyuningtyas, Wen-Hao Chen, Chen-Han Huang, Yu-Jung He, Joseph Jen-Tse Huang
Article
Chemistry, Multidisciplinary
Ruei-Yu He, Xiang-Me Lai, Chia-Sui Sun, Te-Shien Kung, Jhu-Ying Hong, Yu-Song Jheng, Wei-Neng Liao, Jen-Kun Chen, Yung-Feng Liao, Pang-Hsien Tu, Joseph Jen-Tse Huang
Review
Biochemistry & Molecular Biology
Hung-Ming Chien, Chi-Chang Lee, Joseph Jen-Tse Huang
Summary: TDP-43 is a nucleic acid-binding protein with multiple functions, and its low-complexity domain (LCD) plays a crucial role in its functions and involvement in the pathogenesis of neurodegenerative diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
Chemistry, Multidisciplinary
Hung-Ming Chien, Ruei-Yu He, Chi-Chang Lee, Yung-An Huang, I-Ju Hung, Kai-Ting Hou, Jye-Chian Hsiao, Po-Chao Lu, Diksha Agnihotri, Eric Hwang, Joseph Jen-Tse Huang
Summary: This study utilized a photoinducible peptide platform to investigate glycine-alanine dipeptide repeats produced by the C9orf72 gene, revealing that their oligomers can cause cytotoxic effects such as disruption of nuclear membrane and cytosolic retention.
COMMUNICATIONS CHEMISTRY
(2021)
Article
Nanoscience & Nanotechnology
Devi Wahyuningtyas, Wen-Hao Chen, Ruei-Yu He, Yung-An Huang, Chia-Kang Tsao, Yu-Jung He, Chu-Yi Yu, Po-Chao Lu, Yu-Cai Chen, Sheng-Hann Wang, Ka Chon Ng, Bryan Po-Wen Chen, Pei-Kuen Wei, Jiun-Jie Shie, Chun-Hong Kuo, Y. Henry Sun, Joseph Jen-Tse Huang
Summary: The researchers designed and synthesized a polyglutamine-specific gold nanoparticle complex that targeted mHtt and alleviated its toxicity. The complex was able to disassociate fibrillary aggregates from polyQ peptides and reduce beta-sheet content in a concentration-dependent manner. Additionally, the complex was shown to penetrate cells, bind to cytosolic mHtt proteins, dissociate mHtt inclusions, reduce mHtt oligomers, and ameliorate mHtt-induced toxicity, suggesting potential therapeutic strategies against Huntington's disease.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Nanoscience & Nanotechnology
Bryan Po-Wen Chen, Ruei-Yu He, Hung-Ming Chien, Chi-Chang Lee, Hsiao-Han Chuang, Chao-Ping Hsu, Jerry C. C. Chan, Joseph Jen-Tse Huang
Summary: This study reports a method of incorporating hydrazones into amyloidogenic peptides by forming photoisomerizable hydrazones without the need for external reductants or high-power irradiation. Super-resolution microscopy was used to distinguish polymorphic nanoscopic structures of the hydrazone-incorporated peptides in vitro and in live cells.
ACS APPLIED NANO MATERIALS
(2022)
Article
Cell Biology
Lena Eismann, Igor Fijalkowski, Carla Veronica Galmozzi, Jiri Koubek, Frank Tippmann, Petra Van Damme, Guenter Kramer
Summary: This study reveals the role of SecB chaperone protein in co-translational translocation, showing that SecB primarily interacts with inner membrane proteins (IMPs) and other nascent cytoplasmic and translocated proteins, regulated by the chaperone trigger factor. The findings suggest an important function of SecB in protein maturation.
Meeting Abstract
Biochemistry & Molecular Biology
Chi-Chang Lee, Ruei-Yu He, Joseph Jen-Tse Huang
AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
(2019)
Article
Chemistry, Multidisciplinary
Ruei-Yu He, Shu-Han Chao, Yu-Ju Tsai, Chi-Chang Lee, Chu-Yi Yu, Hua-De Gao, Yung-An Huang, Eric Hwang, Hsien-Ming Lee, Joseph Jen-Tse Huang