Article
Microbiology
Paulina A. Fernandez, Marcela Zabner, Jaime Ortega, Constanza Morgado, Fernando Amaya, Gabriel Vera, Carolina Rubilar, Beatriz Salas, Victor Cuevas, Camila Valenzuela, Fernando Baison-Olmo, Sergio A. Alvarez, Carlos A. Santiviago
Summary: By constructing new plasmids, unmarked chromosomal fusions can be generated in Salmonella for studying the expression, secretion, and translocation of T3SS effectors into eukaryotic cells.
Review
Environmental Sciences
Sajjad Hussain, Ping Ouyang, Yingkun Zhu, Abdul Khalique, Changliang He, Xiaoxia Liang, Gang Shu, Lizi Yin
Summary: The failure of traditional vaccination against Salmonella necessitates the development of novel therapeutics. Understanding the role of T3SS in bacterial pathogenesis and the development of anti-virulence agents is crucial, and the inhibition of T3SS at different stages of infection can help in controlling the disease progression. Insights into T3SS inhibitors of Salmonella can mitigate antibiotic resistance and lead to the development of new therapeutics.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Microbiology
Yue Zhang, Honghong Xian, Xi Jiang, Yu Yuan, Ruoyun Ji, Xinan Jiao, Qiuchun Li
Summary: The Sel1-like proteins RS09150 and RS09155 in Salmonella Pullorum SPI-19 contribute to bacterial infection in chickens by mediating the expression of T3SS genes, indicating a potential crosstalk between SPI-19 and T3SS in Salmonella.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Microbiology
Cong Li, Gregory H. Tyson, Chih-Hao Hsu, Lucas Harrison, Errol Strain, Thu-Thuy Tran, Glenn E. Tillman, Uday Dessai, Patrick F. McDermott, Shaohua Zhao
Summary: This study used long-read sequencing to investigate the genomic heterogeneity and antimicrobial resistance mechanisms of Salmonella isolated from retail meats and food animals. It found significant genetic variation among different serotypes, with the presence of plasmids playing a key role in genomic variability. Moreover, the bacteria's resistance mechanisms may be associated with plasmid types, sources, and serotypes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jiaxing Tan, Xing Zhang, Xiaofei Wang, Caihuang Xu, Shenghai Chang, Hangjun Wu, Ting Wang, Huihui Liang, Haichun Gao, Yan Zhou, Yongqun Zhu
Summary: This study provides detailed molecular insights into the structure, assembly, and torque transmission mechanisms of the bacterial flagellar motor.
Article
Biochemical Research Methods
Jessica Nava-Galeana, Cinthia Nunez, Victor H. Bustamante
Summary: The BarA/SirA and Csr regulatory systems control gene expression in bacteria, including the expression of virulence genes. In Salmonella, these systems positively regulate the expression of SPI-1 genes, necessary for bacterial invasion of host cells. Through proteomic analysis, our study identified 164 proteins that are regulated by SirA and CsrB/C in SPI-1-inducing conditions, including 19 potential new targets. This research expands our understanding of the regulatory mechanisms governing the virulence and physiology of an important pathogen.
JOURNAL OF PROTEOMICS
(2023)
Article
Biotechnology & Applied Microbiology
Leyang Wu, Lin Li, Xingpeng Yin, Chenyang Li, Wenjie Xin, Lina Liu, Zichun Hua
Summary: This study developed a potential COVID-19 vaccine strategy using the type III secretion system of attenuated Salmonella and demonstrated its effectiveness. Mixed administration of antigen-expressing strains improved antibody induction, which could be a promising approach for COVID-19 vaccine development.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Alexander S. Balkin, Andrey O. Plotnikov, Natalia E. Gogoleva, Yuri Gogolev, Kirill N. Demchenko, Sergey Cherkasov
Summary: The study revealed the gene expression pattern of Salmonella enterica serovar Typhimurium within Acanthamoeba castellanii, showing downregulation of glycolysis-related genes and upregulation of glyoxylate cycle-related genes, as well as upregulation of genes associated with Salmonella Pathogenicity Island-1, chemotaxis system, and flagellar apparatus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Prashant K. Singh, Gary Cecchini, Terunaga Nakagawa, T. M. Iverson
Summary: The cryoEM structure of a Salmonella MS-ring purified from the assembled flagellar switch complex (MSC-ring) was reported. The post-assembly MS-ring can contain 32, 33, or 34 FliF subunits, with 33 being the most common. RBM3 has a single location with C32, C33, or C34 symmetry, and RBM2 is found in two locations with RBM2(inner) having C21 or C22 symmetry and an RBM2(outer)-RBM1 having C11 symmetry. Comparison to previously reported structures identifies several differences, including the formation of 11 discrete density regions at the base of the structure, differences in interdomain angles in RBM3, and the assignment of amino acids to previously unresolved areas.
Article
Multidisciplinary Sciences
Jieling Wang, Xin Zhu, Zhengmao Wang, Xuecheng Li, Hui Tao, Junmin Pan
Summary: The machinery of intraflagellar transport (IFT) consists of IFT motors and cargo adaptors, including IFT-A and IFT-B complexes. This study reveals the role of IFT38 in the regulation of anterograde IFT and retrograde trafficking of BBSome. The stability of IFT-B1 and IFT-B2 is mutually dependent and mediated by the connecting tetramer IFT38/5788/52. The findings suggest a modular pathway for IFT-B assembly.
Review
Chemistry, Multidisciplinary
Emily Lundstedt, Daniel Kahne, Natividad Ruiz
Summary: The asymmetric lipid bilayer of Gram-negative bacteria's outer membrane is crucial for antibiotic resistance, assembled by specific protein machines such as the Lpt system and Mla pathway.
Article
Multidisciplinary Sciences
Akihiro Kawamoto, Tomoko Miyata, Fumiaki Makino, Miki Kinoshita, Tohru Minamino, Katsumi Imada, Takayuki Kato, Keiichi Namba
Summary: The bacterial flagellar MS ring is a core transmembrane complex within the flagellar basal body. CryoEM analysis suggests that the MS ring is formed by 34 full-length FliF subunits, with 23- and 11-fold subsymmetries in the inner and middle M ring, respectively.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Rerngwit Boonyom, Sittiruk Roytrakul, Patipat Thinwang
Summary: Salmonella enterica serovar Typhimurium (S. Typhimurium) causes infection by injecting effector proteins into host cells through the type III secretion system (T3SS). A small molecule compound, C24H17ClN4O2S, inhibits the T3SS of S. Typhimurium and reduces its invasion ability. The compound blocks the secretion of T3SS by inhibiting the expression of the SPI-1 regulator, InvF.
JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sonia Gomes Pereira, Ana Laura Sousa, Catarina Nabais, Tiago Paixao, Alexander J. Holmes, Martin Schorb, Gohta Goshima, Erin M. Tranfield, Jorg D. Becker, Monica Bettencourt-Dias
Summary: Centrioles in the spermatogenesis of the bryophyte Physcomitrium patens are born through an uncharacterized de novo pathway, showing twisted and asymmetric morphology. This phenomenon reveals that centriole biogenesis is more diverse than previously thought.
Article
Multidisciplinary Sciences
Tomoko Yamaguchi, Fumiaki Makino, Tomoko Miyata, Tohru Minamino, Takayuki Kato, Keiichi Namba
Summary: The study utilizes electron cryomicroscopy to unveil the structure of the LP ring around the rod in the basal body of the bacterial flagellum, shedding light on its stability and assembly mechanisms.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Christoffer Norn, Basile I. M. Wicky, David Juergens, Sirui Liu, David Kim, Doug Tischer, Brian Koepnick, Ivan Anishchenko, Foldit Players, David Baker, Sergey Ovchinnikov
Summary: The protein design problem aims to find an appropriate amino acid sequence for a desired protein structure, with optimization over all possible sequences and structures using protein structure prediction and backpropagation. The trRosetta model is more effective than Rosetta single-point energy estimations, and combining trRosetta and Rosetta models can result in more funneled energy landscapes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, Ivan Anishchenko, Justas Dauparas, David Baker
Summary: DeepAccNet is a deep learning framework that estimates per-residue accuracy and residue-residue distance signed error in protein models, guiding Rosetta protein structure refinement and demonstrating improved accuracy prediction and refinement compared to other methods.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Toshifumi Fujioka, Nobutaka Numoto, Hiroyuki Akama, Kola Shilpa, Michiko Oka, Prodip K. Roy, Yarkali Krishna, Nobutoshi Ito, David Baker, Masayuki Oda, Fujie Tanaka
Summary: The study found that the directionality of protein catalysts can be altered by replacing one amino acid. Additionally, protein catalysts from the same protein scaffold exhibit different efficiency in catalyzing aldol and retro-aldol reactions.
Article
Chemistry, Multidisciplinary
Rebecca Crawshaw, Amy E. Crossley, Linus Johannissen, Ashleigh J. Burke, Sam Hay, Colin Levy, David Baker, Sarah L. Lovelock, Anthony P. Green
Summary: The combination of computational design and directed evolution has shown to be effective in creating enzymes with new functions and catalytic mechanisms for challenging chemical transformations. Through evolutionary optimization of a primitive design, an efficient and enantioselective enzyme was developed for a specific reaction, demonstrating that intricate catalytic devices can be built to promote demanding multi-step processes not observed in nature.
Editorial Material
Biochemical Research Methods
Minkyung Baek, David Baker
Review
Multidisciplinary Sciences
Sarah L. Lovelock, Rebecca Crawshaw, Sophie Basler, Colin Levy, David Baker, Donald Hilvert, Anthony P. Green
Summary: Designing efficient enzymes has a profound impact on chemistry, biotechnology, and medicine. Recent advances in protein engineering and computational methods have made it possible to optimize protein structures and generate efficient enzymes through laboratory evolution. Emerging methods like deep learning hold promise for improving the accuracy of protein design models.
Article
Multidisciplinary Sciences
Shuai Zhang, Robbie Sadre, Benjamin A. Legg, Harley Pyles, Talita Perciano, E. Wes Bethel, David Baker, Oliver Rubel, James J. De Yoreo
Summary: This study directly observes and quantifies the rotational dynamics of protein nanorods on solid-water interfaces using high-speed atomic force microscopy and machine learning techniques. The findings reveal the characteristics of transitions between different angular states and provide insights into the self-assembly and other orientationally anisotropic outcomes of biomolecules at these interfaces.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Sicong Yao, Adam Moyer, Yiwu Zheng, Yang Shen, Xiaoting Meng, Chong Yuan, Yibing Zhao, Hongwei Yao, David Baker, Chuanliu Wu
Summary: Peptide heterodimers are functional macromolecules and molecular tools with wide applications in chemical and synthetic biology. In this study, the authors report the successful design, synthesis, and application of peptide heterodimers with mutual orthogonality through computational de novo designs and a directed disulfide pairing strategy. These heterodimers can be utilized as scaffolds for generating functional molecules, as well as chemical tools or building blocks for protein labeling and crosslinking hybrids.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Brian L. Trippe, Buwei Huang, Erika A. DeBenedictis, Brian Coventry, Nicholas Bhattacharya, Kevin K. Yang, David Baker, Lorin Crawford
Summary: Sort-seq assays are commonly used in biological engineering to profile groups of cells based on their fluorescence characteristics. However, current methods introduce systematic bias. This study demonstrates that unbiased estimates can be obtained by incorporating randomness into the sorting process. The findings are validated through simulations and experiments, and extensions for estimating group level variances and using multi-bin sorters are described.
Article
Biotechnology & Applied Microbiology
Dingchang Lin, Xiuyuan Li, Eric Moult, Pojeong Park, Benjamin Tang, Hao Shen, Jonathan B. B. Grimm, Natalie Falco, Bill Z. Z. Jia, David Baker, Luke D. D. Lavis, Adam E. E. Cohen
Summary: Recording the transcriptional histories of cells can provide a deeper understanding of their developmental trajectory and response to external stimuli. This study introduces an engineered protein fiber that incorporates fluorescent marks to create a ticker tape-like history. By utilizing a reporter gene and high-resolution imaging, the cellular histories can be accurately read and the absolute timing determined. The protein-based ticker tape design has the potential for massively parallel single-cell recordings of various physiological processes.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Thomas W. Linsky, Kyle Noble, Autumn R. Tobin, Rachel Crow, Lauren Carter, Jeffrey L. Urbauer, David Baker, Eva-Maria Strauch
Summary: This study presents a computational platform for designing various small protein folds and sampling shape diversity. Through experimental validation of approximately 30,000 de novo protein designs, about 6,200 stable proteins were identified. The study also revealed protein folding rules and provided training data for machine learning.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Enrico Rennella, Danny D. Sahtoe, David Baker, Lewis E. Kay
Summary: With recent advancements in calculating protein structures from amino acid sequences using AI algorithms, the next important step is to understand how dynamics is encoded in the primary protein sequence to improve function prediction. This study emphasizes the significance of dynamics in modulating the function of a designed protein called C34, which binds β-strands. By investigating the structural dynamics of C34 using NMR spectroscopy, the researchers show that manipulating conformations can enhance functionality in protein design.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H. Abedi, David Baker, Philip Bradley
Summary: This study develops a model for predicting peptide-binding proteins and peptide-MHC interactions by adding a classifier on top of the AlphaFold network. The model shows strong generalization and excellent performance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Sanaa Mansoor, Minkyung Baek, David Juergens, Joseph L. Watson, David Baker
Summary: The study evaluates the performance of the RFjoint model for mutation effect prediction and finds that it achieves comparable accuracy to other models without specific training. RFjoint demonstrates a broad understanding of protein sequence-structure landscapes, making it a useful tool for protein modeling.
Article
Biochemical Research Methods
Minkyung Baek, Ryan Mchugh, Ivan Anishchenko, Hanlun Jiang, David Baker, Frank DiMaio
Summary: Protein-nucleic acid complexes have been a challenge in structure prediction, and this study introduces RoseTTAFoldNA as a method to predict their structures with high accuracy and practical value.