Article
Biochemistry & Molecular Biology
Subbaian Brindha, Yutaka Kuroda
Summary: The use of a solubility-enhancing peptide tag containing nine arginine residues can significantly improve the solubility of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein expressed in Escherichia coli. This discovery has the potential to accelerate the development of anti-COVID-19 therapeutics. The folded RBD-C9R demonstrated binding activity with the host cell receptor and elicited a strong immune response in mice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Marilla Amaranto, Paula Vaccarello, Elisa M. E. Correa, Jose L. Barra, Agustina Godino
Summary: Several intein-based self-cleaving affinity tags were evaluated for expression and purification of recombinant proteins in Escherichia coli. Different tags resulted in different outcomes, with some leading to complete cleavage of the protein while others were unable to release the target protein.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Microbiology
Klaudia Arauzo-Aguilera, Mirva J. Saaranen, Colin Robinson, Lloyd W. Ruddock
Summary: High-value heterologous proteins with disulfide bonds are typically targeted to the periplasm via the Sec pathway, but the Tat system shows potential as an alternative because it can transport fully folded proteins. Previous studies using the TorA signal peptide, a Tat-specific signal peptide, resulted in lower yields and protein degradation. This study demonstrates that the Tat pathway, specifically through the MdoD and AmiC signal peptides, can export the disulfide bond-containing protein YebF to the periplasm and media at high levels.
Article
Biochemistry & Molecular Biology
Subbaian Brindha, Md Golam Kibria, Tomonori Saotome, Satoru Unzai, Yutaka Kuroda
Summary: The study demonstrates that using a SEP tag containing C9R in Escherichia coli can effectively increase the expression yield and purity of EGFR-ECDIII protein. This method enables the production of EGFR-ECDIII with native-like properties and the generation of neutralizing antibodies, showing potential value in anti-cancer therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Richard J. Spears, Alina Chrzastek, Steven Y. Yap, Kersti Karu, Abil E. Aliev, James R. Baker, Vijay Chudasama
Summary: In this study, we report a significant discovery regarding the use of tris(dialkylamino)phosphine reagents in peptide and protein modification. We found that C-terminal thiophosphonium species can be selectively and rapidly generated from their disulfide counterparts, with unique stability. In contrast, internal thiophosphonium species degrade quickly. We demonstrated this chemoselectivity on a model peptide and an antibody fragment, and characterized the species in various small molecule/peptide studies.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Lukas A. A. Rettenbacher, Tobias von der Haar
Summary: This study establishes a novel approach for quantitatively investigating the ability of E. coli to produce disulfide bonds in its proteome. The study shows that the demand for disulfide bonded proteins in E. coli changes significantly under different growth conditions, and predicts under what conditions excess capability is available for recombinant protein production.
MICROBIAL CELL FACTORIES
(2022)
Article
Multidisciplinary Sciences
Guochen Qin, Menghuan Qu, Bei Jia, Wei Wang, Zhuojun Luo, Chun-Peng Song, W. Andy Tao, Pengcheng Wang
Summary: This study developed a highly sensitive method for detecting S-nitrosylation peptides, allowing for quantitative identification of S-nitrosylated proteins and revealing a key role of GSNOR1 in regulating endoplasmic reticulum functions in Arabidopsis.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tetiana Bondarchuk, Vyacheslav F. Shalak, Dmytro M. Lozhko, Agnieszka Fatalska, Roman H. Szczepanowski, Vladyslava Liudkovska, Oleksandr Yu Tsuvariev, Michal Dadlez, Anna El'skaya, Boris S. Negrutskii
Summary: Protein synthesis in eukaryotic cells is compartmentalized, ensuring high efficiency. Higher eukaryotes have stable multi-protein complexes of aminoacyl-tRNA synthetases and translation elongation factors. The human guanine-nucleotide exchange factor (GEF) complex eEF1B is organized in a quaternary structure, with alpha, beta, and gamma subunits forming a heterotrimeric form eEF1B(alpha beta gamma)(3). This unique assembly of GEFs within a stable complex serves as a "GEF hub" that maintains the translationally active GTP-bound conformation of eEF1A in higher eukaryotes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Gregory A. Prussia, Krista A. Shisler, Oleg A. Zadvornyy, Bennett R. Streit, Jennifer L. DuBois, John W. Peters
Summary: The 2-KPCC enzyme, a member of the DSOR family, plays a key role in promoting carboxylation of acetoacetate through the F501H and H506E variants. F501 protects the enolacetone intermediate from protons, while H506 stabilizes the formation of acetoacetate, providing insight into the catalytic mechanism of 2-KPCC. Additionally, the F501H substitution promotes a DSOR-like charge transfer interaction with flavin adenine dinucleotide, eliminating the need for cysteine as an internal base.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Cell Biology
Kaiku Uegaki, Yuji Tokunaga, Michio Inoue, Seiji Takashima, Kenji Inaba, Koh Takeuchi, Ryo Ushioda, Kazuhiro Nagata
Summary: The ER maintains an oxidative redox environment for the folding of nascent polypeptides, while reductive reactions are crucial for ER homeostasis. The mechanism of electrons supply for ER reductase activity is still unknown. This study identifies Ero1a as an electron donor for ERdj5, indicating the contribution of oxidative folding to reductive reactions in the ER and the maintenance of ER homeostasis.
Article
Microbiology
Jonas Schluter, Ana Djukovic, Bradford P. Taylor, Jinyuan Yan, Caichen Duan, Grant A. Hussey, Chen Liao, Sneh Sharma, Emily Fontana, Luigi A. Amoretti, Roberta J. Wright, Anqi Dai, Jonathan U. Peled, Ying Taur, Miguel-Angel Perales, Benjamin A. Siranosian, Ami S. Bhatt, Marcel R. M. van den Brink, Eric G. Pamer, Joao B. Xavier
Summary: TaxUMAP is a visualization tool that allows for the display of microbiome states in large clinical datasets. It was used to create a microbiome atlas of 1,870 cancer patients undergoing therapy-induced perturbations. The tool revealed associations between bacterial density, diversity, and antimicrobial resistance genes. It also identified certain species associated with lower risk for bacteremia, validating a competitive interaction. TaxUMAP provides valuable insights into the effects of the microbiome on human health.
CELL HOST & MICROBE
(2023)
Article
Multidisciplinary Sciences
Elizaveta Krol, Lisa Stuckenschneider, Joana M. Kastle Silva, Peter L. Graumann, Anke Becker
Summary: In Rhizobiales bacteria, such as Sinorhizobium meliloti, cell elongation specifically occurs at new cell poles generated by cell division. The FtsN-like protein RgsS and peptidoglycan amidase AmiC play crucial roles in reliable selection of the new cell pole as the cell elongation zone. Absence of these components can lead to inverted growth polarity and incomplete chromosome segregation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Tong Yang, Feng Gao
Summary: Pan-genome analysis of bacteria provides detailed insights into the diversity and evolution of bacterial populations. However, careful checking of the genomes included in the analysis is necessary to avoid the inclusion of confounding strains. This study found that highly similar strains can also affect the results of unique genes in pan-genome analysis, leading to a significant underestimation of the number of unique genes. Therefore, these strains should be excluded from the analysis in the early stage of data processing.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Subbaian Brindha, Takahiro Yoshizue, Rawiwan Wongnak, Hitoshi Takemae, Mami Oba, Tetsuya Mizutani, Yutaka Kuroda
Summary: This study evaluated the potential of Escherichia coli-expressed receptor-binding domain (RBD) of SARS-CoV-2 as an antigen candidate for a subunit vaccine. The expressed RBD exhibited native-like structure and biophysical properties, and effectively elicited the production of neutralizing antibodies. Additionally, immunization with the E. coli-expressed RBD induced sustained antibody levels and generated multifunctional T cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sebastian Nilewski, Marharyta Varatnitskaya, Thorsten Masuch, Anna Kusnezowa, Manuela Gellert, Anne F. Baumann, Natalie Lupilov, Witali Kusnezow, Markus-Hermann Koch, Martin Eisenacher, Mehmet Berkmen, Christopher H. Lillig, Lars Leichert
Summary: A rational design expression library of metagenomic proteins was created to assign in vivo functions to thousands of proteins, revealing a novel reaction mechanism in a seemingly familiar protein superfamily. The study suggests that the isomerization conformation of a protein may be correlated with its redox activity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)