Article
Multidisciplinary Sciences
Linlin Dong, Song Yang, Jingxia Chen, Xiaofei Wu, Dongjie Sun, Chen Song, Long Li
Summary: Secretory proteins are translocated across lipid membranes via protein-conducting channels called SecY in prokaryotes and Sec61 in eukaryotes. SecA, an ATPase, drives the posttranslational translocation of secretory proteins in bacteria through the SecY channel. The mechanism of how SecA moves a polypeptide chain through the SecY channel is poorly understood. This study presents electron cryomicroscopy structures of the active SecA-SecY translocon with a polypeptide substrate, revealing the conformational changes of SecA and the structural basis of polypeptide movement during translocation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Aaron J. O. Lewis, Ramanujan S. Hegde
Summary: SecY and YidC, as two ancient and essential protein transporters, share previously unrecognized similarities in sequence, structure, mechanism, and function. The detailed correspondence between these two proteins enables a deeper mechanistic understanding of their functions. Furthermore, the key differences between them help explain how SecY performs its distinctive function in recognizing and translocating secretory proteins.
Review
Plant Sciences
Lin Zhang, Jiachao Zhou, Timothy S. George, Erik Limpens, Gu Feng
Summary: More than two-thirds of terrestrial plants form a symbiotic relationship with arbuscular mycorrhizal (AM) fungi to acquire nutrients. The hyphal exudates of AM fungi not only contain carbon-rich compounds, but also promote bacterial growth and activity, and influence microbial community structure, leading to changes in organic nutrient cycling. This makes the hyphosphere an important but often overlooked functional zone in ecosystems.
TRENDS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Eva Pauwels, Neesha R. Shewakramani, Brent De Wijngaert, Anita Camps, Becky Provinciael, Joren Stroobants, Kai -Uwe Kalies, Enno Hartmann, Piet Maes, Kurt Vermeire, Kalyan Das
Summary: During cotranslational translocation, the signal peptide of a nascent chain binds Sec61 translocon to initiate protein transport through the endoplasmic reticulum (ER) membrane. Our cryo-electron microscopy structure of ribosome-Sec61 shows binding of an ordered heterotetrameric translocon-associated protein (TRAP) complex, in which TRAP-gamma is anchored at two adjacent positions of 28S ribosomal RNA and interacts with ribosomal protein L38 and Sec61 alpha/gamma. Four transmembrane helices (TMHs) of TRAP-gamma cluster with one C-terminal helix of each alpha, 13, and delta subunits.
Article
Cell Biology
Zhu Qiao, Tatsuhiko Yokoyama, Xin-Fu Yan, Ing Tsyr Beh, Jian Shi, Sandip Basak, Yoshinori Akiyama, Yong-Gui Gao
Summary: The membrane-bound AAA protease FtsH plays a crucial role in controlling protein quality in bacteria. In this study, the researchers investigated the structure of the FtsH-HfIKC complex, which includes both HfIK and HfIC proteins. They found that 12 copies of HfIK and HfIC interact reciprocally to form a cage-like structure, with FtsH hexamers enclosed inside. The interaction between FtsH and HfIK was shown to be important for complex formation, and comparison with a human protease provided insights into the role of the HfIKC cage in regulating substrate access to FtsH.
Article
Biochemistry & Molecular Biology
Anusha Valpadashi, Sylvie Callegari, Andreas Linden, Piotr Neumann, Ralf Ficner, Henning Urlaub, Markus Deckers, Peter Rehling
Summary: In this study, a crosslinking-mass spectrometry approach was used to determine the molecular arrangement of subunits of the human TIM22 complex, revealing unexpected features and opening up new avenues for a deeper investigation into the steps required for TIM22-mediated translocation in humans.
Review
Biochemistry & Molecular Biology
Eva Pauwels, Ralf Schuelein, Kurt Vermeire
Summary: The process of protein translocation across the ER is mediated by the Sec61 translocon complex, which is challenging to purify and reconstitute, making it difficult to screen for small molecule inhibitors. However, these inhibitors have potential as valuable tools in cell biology and as novel anticancer drugs. Recent screening strategies may also help in identifying new antibiotic drugs targeting the bacterial Sec61 complex counterpart, SecYEG.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Microbiology
Lucy Troman, Ian Collinson
Summary: The article examines the transport process of Gram-negative bacteria inner membrane proteins, as well as the delivery and folding into the periplasm or outer membrane. The mechanism involves interactions between Sec and BAM translocons, possibly with other factors, to provide a conduit to the periplasm and outer membrane.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Pamela Ornelas, Thomas Bausewein, Janosch Martin, Nina Morgner, Stephan Nussberger, Werner Kuehlbrandt
Summary: The TOM complex is the main entry point for precursor proteins into mitochondria. It consists of two beta-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 acts as a dynamic gatekeeper guiding preproteins into the TOM complex.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Meng Yu, Wei Si, Tao Zeng, Chang Chen, Xiaojing Lin, Zhouxiang Ji, Fei Guo, Yuxiang Li, Jingjie Sha, Yuliang Dong
Summary: This research used all-atom molecular dynamic simulations to uncover the microscopic mechanism behind current variation when single-stranded DNA passes through the MspA nanopore. It was found that nucleotide orientation and the region below the constriction of the nanopore play crucial roles in inducing current variation. These findings provide valuable insights for developing low-cost, high-throughput nanopore DNA sequencing technology.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Multidisciplinary Sciences
Katharina Best, Ken Ikeuchi, Lukas Kater, Daniel Best, Joanna Musial, Yoshitaka Matsuo, Otto Berninghausen, Thomas Becker, Toshifumi Inada, Roland Beckmann
Summary: Ribosome collisions can initiate rescue and quality control pathways for aberrant translation. The authors of this study unravel the molecular mechanism of collided ribosome clearance by the ribosome quality control trigger complex. Stalling of ribosomes due to translation of aberrant messenger RNAs can lead to ribosomal collisions. Specifically recognized collided ribosomes initiate stress responses and quality control pathways. Core to this process is the splitting of collided ribosomes by the ribosome quality control trigger complex, RQT, through an unknown mechanism. Cryogenic electron microscopy reveals that RQT engages with the 40S subunit of the lead ribosome and can adopt two conformations. The Ski2-like helicase 1 (Slh1) subunit of RQT is proposed to exert a pulling force on the mRNA, resulting in destabilizing conformational changes of the small ribosomal subunit and subsequent subunit dissociation. These findings provide a conceptual framework for a helicase-driven ribosomal splitting mechanism.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Anna M. Schlagowski, Katharina Knoringer, Sandrine Morlot, Ana Sanchez Vicente, Tamara Flohr, Lena Kraemer, Felix Boos, Nabeel Khalid, Sheraz Ahmed, Jana Schramm, Lena M. Murschall, Per Haberkant, Frank Stein, Jan Riemer, Benedikt Westermann, Ralf J. Braun, Konstanze F. Winklhofer, Gilles Charvin, Johannes M. Herrmann
Summary: The study investigates the regulation of aggregation-prone polyQ protein behavior by mitochondrial processes, revealing that Mia40 plays a rate-limiting role in the import of mitochondrial precursor proteins and can be exploited to stabilize cytosolic proteostasis.
Article
Biochemistry & Molecular Biology
Tsai-Hsuan Weng, Wieland Steinchen, Birgitta Beatrix, Otto Berninghausen, Thomas Becker, Gert Bange, Jingdong Cheng, Roland Beckmann
Summary: The article presents a cryo-EM structure of the yeast Sec complex bound to a substrate and a crystal structure of the Sec62 cytosolic domain. The study revealed that the gate of the Sec complex is in a more open conformation when the signal sequence is inserted, flanked by Sec62 transmembrane helices. The interaction between Sec62 domain and Sec63 C-terminus was also mapped.
Article
Agriculture, Dairy & Animal Science
Yuri Almeida Gomes, L. S. Medeiros, Maria Isabel Nogueira Di Azevedo, Ana Paula Loureiro, Juliana dos Santos Loria de Melo, Filipe Anibal Carvalho-Costa, Walter Lilenbaum
Summary: Genital leptospirosis in pigs can lead to economic losses and reproductive failures. This study identified and analyzed leptospires in the reproductive tracts of female pigs slaughtered in the Amazon region. The results suggest the possibility of venereal transmission and highlight the potential impact of genital leptospirosis syndrome on swine production.
ANIMAL REPRODUCTION SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Shuaikun Su, Yutong Xue, Alexei Sharov, Yongqing Zhang, Seung Kyu Lee, Jennifer L. Martindale, Wen Li, Wai Lim Ku, Keji Zhao, Supriyo De, Weiping Shen, Payel Sen, Myriam Gorospe, Dongyi Xu, Weidong Wang
Summary: This study investigates the post-transcriptional influence of topoisomerase 3 beta (TOP3B) and associated proteins on mRNA translation and turnover. The findings suggest that TOP3B and TDRD3 have a stronger coordination in mRNA regulation compared to FMRP. The study also reveals that TOP3B can stabilize a subset of target mRNAs and has a complex effect on mRNA translation, which is partly linked to its ability to change the topology of mRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Allan Mills, Hai-Tuong Le, Franck Duong
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2016)
Article
Biochemistry & Molecular Biology
Lucien Fabre, Huan Bao, James Innes, Franck Duong, Isabelle Rouiller
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Oncology
Kush Dalal, Fuqiang Ban, Huifang Li, Helene Morin, Mani Roshan-Moniri, Kevin J. Tam, Ashley Shepherd, Aishwariya Sharma, James Peacock, Michael L. Carlson, Eric LeBlanc, Carl Perez, Franck Duong, Christopher J. Ong, Paul S. Rennie, Artem Cherkasov
Article
Biology
Michael Luke Carlson, John William Young, Zhiyu Zhao, Lucien Fabre, Daniel Jun, Jianing Li, Jun Li, Harveer Singh Dhupar, Irvin Wason, Allan T. Mills, J. Thomas Beatty, John S. Klassen, Isabelle Rouiller, Franck Duong
Article
Biochemistry & Molecular Biology
John Young, Franck Duong
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biology
Michael Luke Carlson, R. Greg Stacey, John William Young, Irvinder Singh Wason, Zhiyu Zhao, David G. Rattray, Nichollas Scott, Craig H. Kerr, Mohan Babu, Leonard J. Foster, Franck Duong Van Hoa
Article
Multidisciplinary Sciences
James W. Saville, Lucy Troman, Franck Duong Van Hoa
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2019)
Article
Biology
Gabriella Angiulli, Harveer Singh Dhupar, Hiroshi Suzuki, Irvinder Singh Wason, Franck Duong Van Hoa, Thomas Walz
Article
Biochemical Research Methods
John William Young, Irvinder Singh Wason, Zhiyu Zhao, David G. Rattray, Leonard J. Foster, Franck Duong Van Hoa
JOURNAL OF PROTEOME RESEARCH
(2020)
Correction
Biology
Rebecca M. Hiller, Julius von Kugelgen, Huan Bao, Franck Duong Van Hoa, Eric N. Cytrynbaum
BULLETIN OF MATHEMATICAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
N. Zeytuni, S. W. Dickey, J. Hu, H. T. Chou, L. J. Worrall, J. A. N. Alexander, M. L. Carlson, M. Nosella, F. Duong, Z. Yu, M. Otto, N. C. J. Strynadka
Article
Biochemical Research Methods
Xiao X. Zhang, John William Young, Leonard J. Foster, Franck Duong
Summary: Soluble proteins often interact with membranes to perform important functions, but characterizing these interactions can be challenging due to their transient nature and the poor solubility of phospholipids. In this study, nanodiscs and quantitative proteomics were used to identify lipid-binding proteins in yeast, revealing key players in vesicle trafficking and a member of the Hsp40/J-protein family with specificity for phosphatidic acid. This research showcases the utility of combining proteomics with lipid nanodiscs to uncover unique protein-lipid interactions.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
John William Young, Irvinder Singh Wason, Zhiyu Zhao, Sunyoung Kim, Hiroyuki Aoki, Sadhna Phanse, David G. Rattray, Leonard J. Foster, Mohan Babu, Franck Duong van Hoa
Summary: A method combining peptidisc libraries, chromosomal-level gene tagging technology, affinity purification, and mass spectrometry (AP/MS) can stabilize and identify fragile membrane protein complexes at native expression levels. This method avoids common artifacts and allows for the discovery and stabilization of fragile membrane protein assemblies.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
John William Young, Zhiyu Zhao, Irvinder Singh Wason, Franck Duong van Hoa
Summary: The outer membrane of Gram-negative bacteria is crucial for cell protection and antimicrobial discovery. A new method for isolating the outer membrane proteome has been developed, enabling further studies and potential discovery of antimicrobials.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Allan Mills, Franck Duong
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2017)